Terrorism in Southeast Asia

Since September 2001, the United States has increased focus on radical Islamist and terrorist groups in Southeast Asia, particularly those in the Philippines, Indonesia, Malaysia, Thailand, and Singapore. Southeast Asia has been a base for terrorist operations. Al Qaeda penetrated the region by establishing local cells, training Southeast Asians in its camps in Afghanistan, and by financing and cooperating with indigenous radical Islamist groups. Indonesia and the southern Philippines have been particularly vulnerable to penetration by Islamic terrorist groups.

Members of one indigenous network, Jemaah Islamiyah (JI), which has had extensive ties to Al Qaeda, helped two of the September 11, 2001 hijackers and have confessed to plotting and carrying out attacks against Western targets. These include the deadliest terrorist attack since September 2001: the October 2002 bombing in Bali, Indonesia, that killed approximately 200 people, mostly Westerners. Since the Bali bombing in 2002, crackdowns by various governments in the region—encouraged and in some cases supported by the U.S. government and military—are believed to have weakened JI to such an extent that it essentially is no longer a regional organization, but rather is one confined to Indonesia, with some individuals still operating in the southern Philippines. The degrading of JI’s leadership structure is believed to have altered the group’s strategy. More violent, anti-Western JI members have formed breakaway cells. In September 2009, Indonesian authorities claimed they had killed the leader of one such cell, Noordin Mohammed Top. Noordin is believed to have been responsible for organizing the near-simultaneous July 17, 2009 bombings of the J.W. Marriot and Ritz-Carlton hotels in Jakarta. The bombings were the first successful anti-Western terrorist attack in Indonesia in four years. Their sophistication triggered speculation that Al Qaeda had renewed ties with Top.

To combat the threat, the U.S. has pressed countries in the region to arrest suspected terrorist individuals and organizations, funded and trained Indonesia’s elite counter-terrorist unit, and deployed troops to the southern Philippines to advise the Philippine military in their fight against the violent Abu Sayyaf Group. It has also launched a Regional Maritime Security Initiative to enhance security in the Straits of Malacca, increased intelligence sharing operations, restarted military-military relations with Indonesia, and provided or requested from Congress substantial aid for Indonesia and the Philippines. Also, since 2001, Thailand and the United States have substantially increased their anti-terrorism cooperation.

The responses of countries in the region to both the threat and to the U.S. reaction generally have varied with the intensity of their concerns about the threat to their own stability and domestic politics. In general, Singapore, Malaysia, and the Philippines were quick to crack down on militant groups and share intelligence with the United States and Australia, whereas Indonesia began to do so only after attacks or arrests revealed the severity of the threat to its citizens. Since that time, Indonesian authorities have been aggressive in their pursuit of terrorists and extremist groups. Many governments view increased American pressure and military presence in their region with ambivalence because of the political sensitivity of the issue with both mainstream Islamic and secular nationalist groups. The Muslim insurgency in southern Thailand has escalated in recent years as has terrorist activity in southern areas of the Philippines.

The report looks at the rise of Islamist militancy and the JI network, and discusses terrorism in the region, concluding with options for U.S. policy. Strategies include placing greater emphasis on attacking institutions that support terrorism, building up regional governments’ capacities for combating terrorist groups, and reducing the sense of alienation among Muslim citizens.

Terrorism in Southeast Asia

October 16, 2009 (RL34194)



Since September 2001, the United States has increased focus on radical Islamist and terrorist groups in Southeast Asia, particularly those in the Philippines, Indonesia, Malaysia, Thailand, and Singapore. Southeast Asia has been a base for terrorist operations. Al Qaeda penetrated the region by establishing local cells, training Southeast Asians in its camps in Afghanistan, and by financing and cooperating with indigenous radical Islamist groups. Indonesia and the southern Philippines have been particularly vulnerable to penetration by Islamic terrorist groups.

Members of one indigenous network, Jemaah Islamiyah (JI), which has had extensive ties to Al Qaeda, helped two of the September 11, 2001 hijackers and have confessed to plotting and carrying out attacks against Western targets. These include the deadliest terrorist attack since September 2001: the October 2002 bombing in Bali, Indonesia, that killed approximately 200 people, mostly Westerners. Since the Bali bombing in 2002, crackdowns by various governments in the region—encouraged and in some cases supported by the U.S. government and military—are believed to have weakened JI to such an extent that it essentially is no longer a regional organization, but rather is one confined to Indonesia, with some individuals still operating in the southern Philippines. The degrading of JI's leadership structure is believed to have altered the group's strategy. More violent, anti-Western JI members have formed breakaway cells. In September 2009, Indonesian authorities claimed they had killed the leader of one such cell, Noordin Mohammed Top. Noordin is believed to have been responsible for organizing the near-simultaneous July 17, 2009 bombings of the J.W. Marriot and Ritz-Carlton hotels in Jakarta. The bombings were the first successful anti-Western terrorist attack in Indonesia in four years. Their sophistication triggered speculation that Al Qaeda had renewed ties with Top.

To combat the threat, the U.S. has pressed countries in the region to arrest suspected terrorist individuals and organizations, funded and trained Indonesia's elite counter-terrorist unit, and deployed troops to the southern Philippines to advise the Philippine military in their fight against the violent Abu Sayyaf Group. It has also launched a Regional Maritime Security Initiative to enhance security in the Straits of Malacca, increased intelligence sharing operations, restarted military-military relations with Indonesia, and provided or requested from Congress substantial aid for Indonesia and the Philippines. Also, since 2001, Thailand and the United States have substantially increased their anti-terrorism cooperation.

The responses of countries in the region to both the threat and to the U.S. reaction generally have varied with the intensity of their concerns about the threat to their own stability and domestic politics. In general, Singapore, Malaysia, and the Philippines were quick to crack down on militant groups and share intelligence with the United States and Australia, whereas Indonesia began to do so only after attacks or arrests revealed the severity of the threat to its citizens. Since that time, Indonesian authorities have been aggressive in their pursuit of terrorists and extremist groups. Many governments view increased American pressure and military presence in their region with ambivalence because of the political sensitivity of the issue with both mainstream Islamic and secular nationalist groups. The Muslim insurgency in southern Thailand has escalated in recent years as has terrorist activity in southern areas of the Philippines.

The report looks at the rise of Islamist militancy and the JI network, and discusses terrorism in the region, concluding with options for U.S. policy. Strategies include placing greater emphasis on attacking institutions that support terrorism, building up regional governments' capacities for combating terrorist groups, and reducing the sense of alienation among Muslim citizens.

Terrorism in Southeast Asia

The Rise of Islamist Militancy in Southeast Asia


While there has been significant anti-Western terrorist activity in Southeast Asia, counter-terror measures in recent years appear to have significantly degraded anti-Western terrorist groups' ability to launch attacks against Western targets in the region. U.S. attention in the region has been focused on radical Islamist groups, particularly the Jemaah Islamiyah (JI) terrorist network, that are known or alleged to have ties to the Al Qaeda network. Many of these groups threaten the status quo of the region by seeking to create independent Islamic states in majority-Muslim areas, overthrow existing secular governments, and/or establish a new supra-national Islamic state encompassing Indonesia, Malaysia, Singapore, the southern Philippines, and southern Thailand. In pursuit of these objectives, they have planned and carried out violent attacks against American and other Western targets as well as against Southeast Asian targets. Additionally, Al Qaeda used its Southeast Asia cells to help organize and finance its global activities—including the September 11 attacks—and to provide safe harbor to Al Qaeda operatives, such as the convicted organizer of the 1993 bombing of the World Trade Center, Ramzi Yousef.1 Years of surveillance, arrests, and killings of JI members by various states are believed to have seriously weakened the organization, degrading its command, communication, and fundraising structures to the point where many analysts believe it operates almost exclusively in Indonesia, with a number of operatives also active in Mindanao Philippines.

Combating anti-American terrorism in Southeast Asia presents the Obama Administration and Congress with a delicate foreign policy problem, though not of the highest priority given U.S. engagement in places such as Afghanistan and Iraq. Most regional governments feel threatened by home-grown or imported Islamic militant groups and therefore have ample incentive to cooperate with the U.S. antiterrorist campaign. Despite mutual interests in combating terrorism, Southeast Asian governments have to balance these security concerns with domestic political considerations. Although proponents of violent, radical Islam remain a very small minority in Southeast Asia, many governments view increased American pressure and military presence in their region with concern because of the political sensitivity of the issue with both mainstream Islamic and secular nationalist groups. The rise in anti-American sentiment propelled by both the U.S.-led invasion of and presence in Iraq and many Southeast Asian Muslims' perceptions of America's stance on the Israeli-Palestinian conflict as "blatantly pro-Israel" makes it even more difficult for most governments to countenance an overt U.S. role in their internal security.2 A U.S. foreign policy challenge is to find a way to confront the terrorist elements without turning them into heroes or martyrs in the broader Southeast Asian Islamic community. Furthermore, any evidence of continued activities of Al Qaeda and Jemaah Islamiyah will require a coordinated, international response in a region where multinational institutions and cooperation are weak.

Southeast Asia has been the home of indigenous Islamic militant groups for decades. Traditionally, the linkages among these groups were relatively weak, and most operated only in their own country or islands, focusing on domestic issues such as promoting the adoption of Islamic law (sharia) and seeking independence from central government control.

The emergence of radical Islamic movements in Southeast Asia in the 1990s can be traced to the conjunction of several phenomena. Among these were reaction to globalization—which has been particularly associated with the United States in the minds of regional elites—frustration with repression by secularist governments, the desire to create a pan-Islamic Southeast Asia, reaction to the Israeli occupation in the West Bank and Gaza Strip, and the arrival of terrorist veterans of years of fighting in Afghanistan.

Southeast Asian terrorist and militant groups can be placed on a spectrum that spans the relatively narrow goals and objectives of the separatist Muslims in Southern Thailand or Southern Philippines to the global anti-Western agenda of Al Qaeda. In between can be placed groups such as JI, that have an internal debate over the relative emphasis on achieving an Islamist agenda within individual states as opposed to focusing their fight directly against Western targets. These groups, as well as others such as the Abu Sayyaf Group, will be explored in greater detail below.

The Rise of Al Qaeda in Southeast Asia

Beginning in the early-to-mid 1990s the Al Qaeda terrorist network made significant inroads into the Southeast Asia region. Al Qaeda's Southeast Asian operatives—who have been primarily of Middle Eastern origin—appear to have performed three primary tasks. First, they set up local cells, predominantly headed by Arab members of Al Qaeda, that served as regional offices supporting the network's global operations. These cells have exploited the region's generally loose border controls to hold meetings in Southeast Asia to plan attacks against Western targets, host operatives transiting through Southeast Asia, and provide safe haven for other operatives fleeing U.S. intelligence services. Al Qaeda's Manila cell, which was founded in the early 1990s by a brother-in-law of Osama bin Laden, was particularly active in the early-mid-1990s. Under the leadership of Ramzi Yousef, who fled to Manila after coordinating the 1993 bombing of the World Trade Center in New York, the cell plotted to blow up 11 airliners in a two-day period (what was known as the "Bojinka" plot), crash a hijacked airliner into the Central Intelligence Agency's headquarters, and assassinate the Pope during his visit to the Philippines in early 1995. Yousef was assisted in Manila for a time by his uncle, Khalid Sheikh Mohammed, the alleged mastermind of the September 11, 2001 attacks.3 In the late 1990s, the locus of Al Qaeda's Southeast Asia activity appears to have moved to Malaysia, Singapore, and—most recently—Indonesia. In 1999 and 2000, Kuala Lumpur and Bangkok were the sites for important strategy meetings among some of the September 11 plotters.4 Al Qaeda's leadership also has taken advantage of Southeast Asia's generally loose financial controls to use various countries in the region as places to raise, transmit, and launder the network's funds. By 2002, according to expert opinion on Al Qaeda, roughly one-fifth of Al Qaeda's organizational strength was centered in Southeast Asia.5

Second, over time, Al Qaeda Southeast Asian operatives helped create what may be Southeast Asia's first indigenous regional terrorist network, Jemaah Islamiyah, which has plotted attacks against Western targets. Jemaah Islamiyah is believed to have carried out the October 12, 2002 bombing in Bali, Indonesia, that killed approximately 200 people, mostly Western tourists. Although JI does not appear to be subordinate to Al Qaeda, the two networks have cooperated extensively.

Third, Al Qaeda's local cells worked to cooperate with indigenous radical Islamic groups by providing them with money and training. Until it was broken up in the mid-1990s, Al Qaeda's Manila cell provided extensive financial assistance to Moro militants such as the Abu Sayyaf Group and the Moro Islamic Liberation Front (MILF). Thousands of militants have reportedly been trained in Al Qaeda camps in Afghanistan or in the camps of Filipino, Indonesian, and Malaysian groups that opened their doors to Al Qaeda. Al Qaeda reportedly provided funds and trainers for camps operated by local groups in Indonesia, Malaysia, and the Philippines. Indonesian intelligence officials also accuse Al Qaeda of sending fighters to participate in and foment the Muslim attacks on Christians in the Malukus and on Sulawesi that began in 2000.6 Al Qaeda operatives' task was made easier by several factors including the withdrawal of foreign state sponsors, most notably Libya, that had supported some local groups in the 1970s and 1980s; the personal relationships that had been established during the 1980s, when many Southeast Asian radicals had fought as mujahideen in Afghanistan; and weak central government control. Other factors included endemic corruption, porous borders, minimal visa requirements, extensive networks of Islamic charities, and lax financial controls of some countries, most notably Indonesia and the Philippines.7

Over time, Al Qaeda's presence in the region has had the effect of professionalizing local groups and forging ties among them—and between them and Al Qaeda—so that they can better cooperate. In many cases, this cooperation has taken the form of ad hoc arrangements of convenience, such as helping procure weapons and explosives.

The Jemaah Islamiyah Network

In the weeks after the September 11, 2001 terrorist attacks, the full extent of the pan-Asian terrorist network with extensive links to Al Qaeda was uncovered. The network, known as Jemaah Islamiyah (Islamic Group), was discovered to have cells in Indonesia, Malaysia, the Philippines, Singapore, and Thailand as well as in Australia and Pakistan. Since the Bali bombing in 2002, which JI is suspected of carrying out, crackdowns by various governments in the region are believed to have severely weakened the organization.

Arrests and killings by Indonesian authorities in 2007 are thought to have been particularly effective, as was the reported 2009 killing of Noordin Mohammed Top. Some analysts now believe JI is no longer a regional organization, in that its administrative structure appears to be confined to Indonesia. Even there, JI apparently was unable to muster forces to combat a January 2007 crackdown by police in the Central Sulawesi district of Poso that appears to have driven JI from the area. JI's links to Al Qaeda reportedly have withered. Most analysts caution, however, that individual JI members remain scattered across the region, are highly trained, and are capable of carrying out acts of violence. Additionally, JI's more moderate factions appear to have refocused on grass-roots education, indoctrination, and other activities they feel are better suited to their long-term goal of instituting sharia law in Indonesia.8 Therefore, JI's activities in the medium to long term bear watching.

JI's goals have ranged from establishing an Islamic regime in Indonesia, to establishing an Islamic caliphate over Muslim regions of Southeast Asia and northern Australia, to waging jihad against the West. Until the more militant factions either were eliminated or broke away from the organization in the 2005-2007 period, there appears to have been considerable debate within the organization about which of these goals to pursue and prioritize, with different JI factions preferring different objectives. Jemaah Islamiyah leaders have formed alliances with other militant Islamist groups to share resources for training, arms procurement, financial assistance, and to promote cooperation in carrying out attacks.

Indeed, there is some evidence that such cooperation increased after 2002, when arrests and other counterterror actions began to take its toll on JI, forcing it to adapt and form closer working relationships with other groups. Within Indonesia, some in the network have created and/or trained local radical Islamist groups that have been involved in sectarian conflict in the country's outer islands. Additionally, there is considerable evidence that JI has engaged in joint operations and training with Filipino groups. For a time, JI's main partner in the Philippines reportedly was the separatist group, the Moro Islamic Liberation Front (MILF). There is growing cooperation among the Abu Sayyaf Group, several major MILF commands, and elements of JI on Mindanao. According to a 2009 International Crisis Group report, some JI members appear to have made Mindanao a primary base of operations. Others are reportedly working with Abu Sayyaf in Jolo.9

In October 2002, the United States designated JI as a foreign terrorist organization. Thereafter, the United Nations Security Council added the network to its own list of terrorist groups, a move requiring all U.N. members to freeze the organization's assets, deny it access to funding, and prevent its members from entering or traveling through their territories. Since December 2001, over 250 suspected and admitted JI members, including a number of key leaders, have been arrested. Many of these arrests are credited to more extensive intelligence sharing among national police forces.

History of Jemaah Islamiyah

The origins of the Jemaah Islamiyah network stretch back to the 1960s, when its co-founders, clerics Abu Bakar Baasyir and Abdullah Sungkar, began demanding the establishment of sharia law in Indonesia. The two considered themselves the ideological heirs of the founder of the Darul Islam movement, the Muslim guerilla force that during the 1940s fought both imperial Dutch troops and the secularist Indonesian forces of Sukarno, Indonesia's founding President who ruled from 1950 to 1965. In the 1970s, the two men established Al Mukmin, a boarding school in Solo, on the main island of Java, that preached the puritanical Wahhabi interpretation of Islam founded and propagated in Saudi Arabia. Many suspected JI activists who have been arrested are Al Mukmin alums. In 1985, Baasyir and Sungkar fled to Malaysia, where they set up a base of operations and helped send Indonesians and Malaysians to Afghanistan, first to fight the Soviets and later to train in Al Qaeda camps. Sungkar and Baasyir formed JI in 1993 or 1994, and steadily began setting up a sophisticated organizational structure and actively planning and recruiting for terrorism in Southeast Asia. Sometime in the mid-1990s, Sungkar and Baasyir apparently began to actively coordinate with Al Qaeda.

The fall of Indonesia's Suharto regime in 1998 provided a major boost to JI.10 Almost overnight, formerly restricted Muslim groups from across the spectrum were able to operate. Baasyir and Sungkar returned to Solo, preaching and organizing in relative openness there. Simultaneously, Jakarta's ability to maintain order in Indonesia's outer islands decreased dramatically, and long-repressed tensions between Muslims and Christians began to erupt. In 1999 and 2000, the outbreak of sectarian violence in Ambon (in the Malukus) and Poso (on Sulawesi) provided JI with critical opportunities to recruit, train, and fund local mujahideen fighters to participate in the sectarian conflict, in which hundreds died.11 After the violence ebbed, many of these jihadis became active members in Baasyir's network. In 2000, the network carried out bombings in Jakarta, Manila, and Thailand.

Jemaah Islamiyah's Relationship to Al Qaeda

There has been considerable debate over the relationship between Jemaah Islamiyah and Al Qaeda. Although many analysts at first assumed that JI is Al Qaeda's Southeast Asian affiliate, reports—including leaks from interrogations of captured JI and Al Qaeda operatives—have shown that the two groups are discrete organizations with differing, though often overlapping, agendas.12 Whereas Al Qaeda's focus is global and definitively targets the West, Jemaah Islamiyah is focused on radicalizing Muslim Southeast Asia (starting with Indonesia) and some JI leaders are said to feel that attacking Western targets will undermine this goal. After the arrests, deaths, defections, and/or marginalization of more militant members in the middle part of the decade, JI's known links to Al Qaeda reportedly have dwindled to almost nothing.13

That said, the two networks have developed a highly symbiotic relationship. There is reportedly some overlap in membership. They have shared training camps in Pakistan, Afghanistan, and Mindanao. Al Qaeda has provided JI with considerable financial support.14 They shared personnel, such as when JI sent an operative with scientific expertise to Afghanistan to try to develop an anthrax program for Al Qaeda.15 The two networks have jointly planned operations—including the September 11 attacks—and reportedly have conducted attacks in Southeast Asia jointly.16 Often, these operations took the form of Al Qaeda's providing funding and technical expertise, while JI procured local materials (such as bomb-making materials) and located operatives.17 Riduan Isamuddin, also known as Hambali, appears to have been a critical coordinator in these joint operations, and his arrest in 2003 may have curtailed JI-Al Qaeda cooperation, which according to one prominent expert, Sidney Jones, was closest between 1997 and 2002.18 The sophistication of the simultaneous July 2009 hotel bombings in Jakarta (discussed in "The July 2009 Jakarta Hotel Bombings") triggered speculation that Al Qaeda had renewed ties with some Indonesian radicals, particularly the cell led by Noordin Mohammed Top. Noordin's death has raised hopes that these links may again wither.

Jemaah Islamiyah's Size and Structure

The total number of core Jemaah Islamiyah members at its peak was estimated to range from 500 to several thousand.19 Its influence transcends these numbers, however. Many more men have been educated at JI-run pesantrens (religious boarding schools), where Baasyir's and Sungkar's radical interpretation of Islam is taught. JI also has avidly sought out alliances—which at times have been ad hoc—with a loose network of like-minded organizations, and JI-run training camps have upgraded the military skills and ideological fervor of smaller, localized groups.

Interrogations of Jemaah Islamiyah members have revealed a highly formalized command structure, at least during the early part of the decade. JI was led in 2000-2001 by a five-member Regional Advisory Council chaired by Hambali. Baasyir and Sungkar served as spiritual advisors. Beneath the council were several functional committees and four mantiqis (loosely translated as regional brigades) that were defined not only by geography but also by functional roles, including fundraising, religious indoctrination, military training, and weapons procurement. Each mantiqi, in turn, was subdivided into at least three additional layers: battalions, platoons, and squads.20

However, in practice, even at its peak JI appeared to function in a much less centralized fashion than this structure might imply. The network's goal of developing indigenous jihadis meant that JI members often have worked with and/or created local groups outside its control. It often is difficult to sort out the overlap among JI and other radical groups. Additionally, regional leaders appear to have had a fair amount of autonomy, and by necessity many of the individual cells were compartmentalized from one another. The arrest of many if not most of JI's top leaders appears to have accentuated these decentralized tendencies by disrupting the network's command and control structure.

Finally, JI's structure has expanded and contracted in response to internal and external developments. Indonesia expert Sidney Jones has written that since 2002, a more flexible structure, "better suited for an organization under siege," undoubtedly has evolved.21 Many analysts believe that years of arrests have weakened JI to such an extent that it essentially is no longer a regional organization, but rather is one confined to Indonesia, with some individuals still operating in the southern Philippines. The degrading of JI's leadership structure is believed to have led to the sprouting of splinter, semi-independent cells many of which have competing agendas.22 Noordin Mohammad Top, the suspected mastermind of the 2005 and 2009 Jakarta hotel bombings as well as the 2005 Bali terrorist attack, is believed to have led such a faction that is thought to include dozens of current and former JI members, as well as individuals who have no known affiliation with JI. In September 2009, Indonesian police claimed they killed Top in a raid in Central Java.

The breakdown of JI's hierarchy also may have been exacerbated by tensions between two factions over the best means for waging jihad, though it is unclear whether the differences are over tactics or overall strategy. The Singapore-Malaysia mantiqi, led by Hambali until his capture, was interested in focusing on a broader anti-Western agenda similar to al Qaeda, and in effecting change in the near term. Surveillance, arrests, and executions of this group's members and key leaders are believed to have seriously weakened this faction. Noordin derived from this group.23

Opposing this faction is a majority group within JI, depicted as the "bureaucrats," that sees the anti-western focused militants' tactics as undermining its preferred, longer-term strategy of building up military capacity and using religious proselytization to create a mass base sufficient to support an Islamic revolution in the future.24 Likewise, there appears to be divisions among JI members about geographic objectives, with some seeking to establish a Islamic state in Southeast Asia and others focused solely on establishing an Islamic state in Indonesia.25 The implication is that JI may not be as monolithic as commonly assumed.26

Major Plots

Jemaah Islamiyah first came to public attention in December 2001, when Singapore's Internal Security Department (ISD) raided two Singapore cells for plotting bombing attacks against American, Australian, British, and Israeli installations and citizens in Singapore. A video tape subsequently found by U.S. forces in Afghanistan confirmed Al Qaeda's involvement in the plot. Follow-on arrests netted plotters in Malaysia and the Philippines. The JI cell in Malaysia reportedly coordinated the plot, including the procurement of bomb-making materials, preparing forged travel documents, and communications with Al Qaeda.

Subsequent investigation and arrests led the FBI to link Jemaah Islamiyah to the September 11 attack on the United States. Two of the September 11 hijackers and Zacarias Moussaoui, who pled guilty in April 2005 to U.S. charges of involvement in the September 11 plot, visited Malaysia and met with cell members in 2000. Additionally, the FBI claims that Malaysian cell members provided Moussaoui with $35,000 and a business reference.

In June 2002, the Indonesian police arrested a suspected Al Qaeda leader, Kuwaiti national Omar Al-Farouq, at the request of the CIA and turned him over to the U.S. military. After three months of interrogation, Al-Farouq reportedly confessed that he was Al Qaeda's senior representative in Southeast Asia and disclosed plans for other terrorist attacks against U.S. interests in the region. These included a joint Al Qaeda/JI plan to conduct simultaneous car/truck bomb attacks against U.S. interests in Indonesia, Malaysia, Singapore, the Philippines, Thailand, Taiwan, Vietnam, and Cambodia around the first anniversary of the September 11 attacks.27 On the basis of this and other information, in September 2002, the Bush Administration closed U.S. embassies in several countries for several days and raised the overall U.S. threat level from "elevated" (yellow) to "high" (orange). Under interrogation, Al-Farouq reportedly identified Baasyir as the spiritual leader of JI and one of the organizers of the planned September 2002 attacks. In July 2005, Al-Farouq and other suspected Al Qaeda members escaped from a U.S. military detention center in Bagram, Afghanistan. In September 2006, he was killed in Basra, Iraq, during a shootout with British troops.28 (See the Indonesia section below for more information on the Bali bombings and other attacks in Indonesia.)


Recent Events

The July 2009 Jakarta Hotel Bombings

On July 17, 2009, near-simultaneous bombings of the J.W. Marriot and Ritz-Carlton hotels in Jakarta killed nine and injured more than 50, including 6 Americans. The bombings were the first successful anti-Western terrorist attack in Indonesia in four years. They are believed to have been planned by Noordin Mohammad Top, a Malaysian who is a member of JI's more radical, anti-Western faction. As mentioned above, Indonesian police are believed to have killed Noordin in a raid in Central Java in September 2009.

Noordin's precise relationship to JI is unclear and appears to have been in flux. Most analysts appear to believe that he was no longer part of JI's command structure, and that not all of his followers belong to JI. However, most of his followers appear to have been educated in JI-affiliated madrassas and networks, members of the JI network continued to provide him with sanctuary, enabling Noordin to elude arrest for years.29

Analysts also have said that discovering how the bombings were funded will be a key indicator of the state of JI and perhaps Al Qaeda's strength, strategy, and involvement in Indonesia. If the funding sources are found to have come from outside Indonesia or outside Southeast Asia, this may be an indication that at least some factions within JI have decided to hit Western targets again, or that Al Qaeda has potentially reestablished links with Southeast Asia, perhaps through Pakistan or North Africa-based liaisons.30 One report has indicated that funding for recent bombings in Indonesia may have come from Saudi Arabia.31

A development some find worrisome along these lines is that Noordin's faction changed its name to the Al-Qaeda Jihad Organisation for the Malay Archipelago, though it is unclear whether this represents the re-establishment of operational links or is merely a ploy to attract radical adherents. Before Noordin's alleged death, the International Crisis Group estimated his following to be in the "dozens."32 According to Sydney Jones, Noordin's group modeled itself "… in terms of ideology, targets, and propaganda, after Al-Qaeda." Jones described the central question after the bombings as whether Noordin was imitating Al-Qaeda or whether he had developed some "structural affiliation" with Al Qaeda.33

Indonesian police have reportedly been pursuing connections between the July bombings and Al-Qaeda. Indonesian National Police Chief Bambang Hendarsono Danuri stated that Mohammed Jibril Abduahman was once a member of Al Qaeda. Jibril was arrested in July on suspicion of facilitating the funding of the July bombings. Jibril studied Islam in Karachi, Pakistan where he is thought to have joined the Al-Qaeda affiliated group Al-Ghuraba.34

Some have attributed a "terror resurgence" in Southeast Asia to increased linkages between intra-regional groups, such as JI and Abu Sayyaf. Singapore-based terrorism analyst Rohan Gunaratna has stated that the Indonesian terrorist groups and Abu Sayyaf are "operating almost as one organization."35

The July 2009 bombings were the first large-scale anti-Western attack in Indonesia since the second Bali bombing of October 2005. This was interpreted as a sign of JI's degraded operational capability. The United States lifted its travel warning on Indonesia in May 2008. U.S. Ambassador to Indonesia Cameron Hume stated that the warning, which was first issued in November 2000, was lifted due to "objective improvements made by Indonesia in its current security situation."36

Despite the July bombings, Indonesian authorities believe they have seriously damaged JI. Detachment 88 is the Indonesian national police force's main counter-terror unit and is thought responsible for much of the success that Indonesia has had in arresting hundreds suspects of which many have been tried and convicted. In May 2008, an associate of Noordin Top, Faiz Fauzan, was apprehended by Indonesian authorities. Fauzan is thought to have had a role in the Bali bombing of 2005.37 JI was also declared an illegal organization by an Indonesian judge in a terrorism trial in April of 2008.38 Indonesia has also reportedly had success through its program of deradicalisation which seeks to bring both the extremist and their families back into the fold of normal society in addition to preventing, deterring, and punishing terrorists.39

Michael Mukasey, then U.S. Attorney General, praised Indonesia's efforts in combating terrorism during a visit to Jakarta in June 2008.

Like Indonesia, the United States has faced terrorist threats and terrorist attacks. We share the challenge of combating violent extremists, while protecting basic civil liberties in the process. Indonesia has been effective in the apprehension and conviction of terrorists and extremists organizations.40

In March 2008, Acting Director of the National Counterterrorism Center Michael Leiter stated "Southeast Asia continues to be a concern, although not nearly that which we might have envisioned two or three years ago."41

Indonesia also has strong bilateral counter-terror cooperation with Australia. During a June 2008 visit to Indonesia, Australian Prime Minister Rudd stated that he and Indonesian President Susilo Bambang Yudhoyono agreed to expand security cooperation within the framework of the Lombok Treaty of 2006. He stated "... we've responded [to terrorist attacks] by strong practical cooperation preventing terrorism and tracking down the perpetrators ... I want to pay special tribute to the close cooperation we have in this area ... The government that I lead is committed to maintaining and strengthening that security cooperation."42

Capture of Noordin Top and Militant Leadership Transition

Following the July bombings, Indonesian police were successful in thwarting a plan to assassinate President Yudhoyono. Police raids in mid-August uncovered a militant network and disrupted plans for attacks that included a plan to carry out a suicide attack on the President's home with a minibus packed with explosives. The uncovering of the plan to kill Yudhoyono reportedly further intensified Indonesian efforts to capture Top.43

After eluding capture for over seven years Top was reportedly killed during a raid by Indonesian police on his hideout in central Java on September 17, 2009. At the conclusion of the six-hour shootout a laptop computer was found at the location that reportedly established linkages between Indonesian militants and Al Qaeda.44 The laptop also reportedly contained information stating that militant Jaelani was recruited by Al Qaeda while studying in Yemen. The information also indicated that Bali remained a key target for militants in Indonesia and that they were also planning an effort to trigger communal conflict between Christians and Muslims in Indonesia.45

It is reported that Syaifudin Zuhri bin Ahmad Jaelani, who is thought to have recruited the suicide bombers for the July 17 hotel bombings, will replace Top as the leader of his JI splinter group. Syaifudin is thought to have become radicalized while in Yemen between 1995 and 2000. Several counter-terrorism experts have expressed the view that Syaifudin could be "equally capable" of leading Top's network.46

Indonesian Anti-Terror Effort Intensifies

The government of Indonesia sought to introduce tougher anti-terror measures in the wake of the July 2009 bombings in Jakarta. These measures include stronger laws that would lengthen detentions for suspects. This would require amendment of the 2002 anti-terror laws. Human rights advocates pointed to the potential that such laws could be abused.47 Some have cautioned that more draconian measures could "radicalize more would-be militants while driving extremists underground."48 President Yudhoyono has also indicated that he intends to use the armed forces in the struggle against militants. Previously only police and special police units have been focused on counter terror operations. Kopassus special forces played a key role in suppressing Islamist forces under the authoritarian regime of former President Suharto.49

Trial of JI leaders

An Indonesian court handed out 15-year sentences to Abu Dujana and Zarkasih in April 2008. The South Jakarta District Court that sentenced Abu Dujana and Zarkasih declared JI a "forbidden corporation" for the first time and found it guilty of being an organization that permits terrorism. The two JI leaders were captured in June 2007. Zarkasih was JI head for Mantique II and was thought to be the defacto head of JI since 2004. Abu Dujana was head of JI's military wing. They were convicted for harboring terrorists and on firearms charges. Dujana was convicted for harboring Muhammad Top who is thought to be one of the leaders behind the Bali bombing who has yet to be captured.50 Their sentencing is viewed by many as a key success for Indonesia's counter-terror effort.51 Dujana is alleged to have had a role in the Marriott bombing, the Jakarta Australian Embassy bombing, and the 2002 Bali bombing.

Political Extremism and Violence in Indonesia

Violence and fear continue to be used by radical Islamists to try to coerce the Indonesian government to change policy to facilitate an Islamist agenda. Members of the Front Pembela Islam (FPI), or Islamic Defenders Front (IDF), attacked a group of peaceful demonstrators on June 1, 2008, who were demonstrating at The National Monument in Jakarta in support of tolerance and moderation regarding efforts by Muslim hardliners to have the Ahmadiyah sect banned in Indonesia. Ahmadiyah believe Mohammad was a prophet but not the last one. As such, their beliefs are inconsistent with the beliefs of other Muslims. The police were reportedly reluctant to intervene to stop the June 1 attacks despite reportedly being present in large numbers. Following the attack IDF leader Habib Rizieq called on his followers to "prepare for war with Ahmadiyah and its followers" unless a ban was enacted by the government.52

Several days after the attack the government reacted to Indonesian moderates' outrage by arresting members of the FPI but also bowed to pressure from extremists and placed a partial ban on the Ahmadiyah. Observers believe this demonstrates that the government remains somewhat reluctant to alienate hardline Muslims and will act to placate them. Some have expressed concern that a message that may be conveyed is that extremists can advance their cause through violence. It is also worth noting that the government reacted to address in part moderate concerns with the incident by arresting FPI members responsible for the violence.53

While inter-communal violence elsewhere in Indonesia has been significantly reduced in recent years, there are signs that inter-communal violence between Christians and Muslims could erupt in Papua or elsewhere. A June 2008 International Crisis Group report stated "violence was narrowly averted in Manokwari and Kaimana in West Papua Province in 2007, but bitterness remains." Dispute over plans developed in 2005 to build a Mosque on the site where German Missionaries brought Christianity to Papua in the 19th century has angered the Papuan Christian community. It also appears that this religious fault line is related to ongoing migration of Muslims to Papua and West Papua from elsewhere in Indonesia.54 Indonesia's recent history has demonstrated that Islamist extremists and terrorists have used inter-communal strife in the past, in places such as Ambon and Poso in the Malukus and on Sulawesi, as a means of mobilizing support for their cause and as a way of recruiting members.


In August 2007, Indonesian President Yudhoyono in his State of the Union address stated "the acts of terrorism that have caused unrest in our society in the past years have been handled.... We have succeeded in preventing and tackling the acts of terrorism in the country." He went on to add that more needs to be done to address the root causes of terrorism including "poverty, injustice, extremism, and a culture of violence."55 His statement follows the June 2007 capture of JI Emir Zarkarsih and JI military leader Abu Dujana. In his speech, Yudhoyono stated that the security situation in Sulawesii and the Malukus had improved.

Statements by captured JI leader Abu Dujana have been interpreted by some to confirm that there has been a split in JI between those within the organization who wish to focus on attacking Western targets, which would include former followers of now deceased Noordin Top's splinter cell, and those who wish to focus their activities on effecting change in Indonesia. Though many find that success by the Indonesian government does appear to have significantly disrupted JI organization and degraded JI capabilities in Indonesia, JI has not been eliminated, and may yet regroup further and conduct additional operations in Indonesia in the future.56 To address this, some analysts have cautioned policy makers against complacency and urged further effort to deny loosely governed regions, particularly in Mindanao in the Philippines and Southern Thailand from being used by terrorist groups.57

Indonesia's attractiveness to Islamist terrorist groups appears to derive primarily from relatively weak central government control and considerable social and political instability and its overwhelmingly Muslim population. Indonesia's central government was weakened by the 1997-1999 Asian financial crisis. The replacement of the authoritarian regime of President Suharto in 1998, which had been in power since 1965, with a more democratic but weaker central government weakened its ability to marginalize Islamist elements within Indonesian society. Indonesia's former President Megawati Sukarnoputri, who was under pressure from Islamic political parties, condemned anti-American violence and pledged to protect U.S. assets and citizens but also publicly opposed the U.S.-led military campaigns in Afghanistan and Iraq.58 The election of Susilo Bambang Yudhoyono in 2004 has led the Indonesian central government to be both more assertive and more effective in its counterterrorist activities. Muslim-Christian strife in the country's remote regions has attracted the involvement of foreign Islamist radicals, including, apparently, some with Al Qaeda connections.

Although the overwhelming majority of Muslim Indonesians follow a moderate form of Islam, fundamentalist Islamic theology is growing in popularity in Indonesia, and radical groups have grown in influence by taking advantage of the country's internal problems. These include separatist movements, a severe economic recession following the Asian financial crisis, problems associated with the evolving reform process, and clashes between Christians and Muslims. The as yet unresolved tension between Christian and Muslim communities in Sulawesi and the Malukus offers terrorists a conflict that they may be able to manipulate to further their ends.59

Even the more extreme groups traditionally have been concerned primarily with domestic issues such as promoting the adoption of Islamic law (sharia). Only a small minority of the Muslim parties favor Islamist agendas. A 2007 Pew Research Poll found that support for suicide bombings and other forms of violence against civilians in defense of Islam had dropped significantly in Indonesia in recent months.60 The U.S.-led campaign against terrorism and the war in Iraq have had negative political resonance in Indonesia. While 95% of Indonesians supported religious tolerance, about 3% still supported bombings and attacks against non-Muslims.61 Although a small percentage, this equates to a large number of individuals in a nation of some 235 million people.

The Bali Bombings and Other JI attacks in Indonesia

The danger posed by Jemaah Islamiyah and Al Qaeda was underscored by the October 12, 2002 bombings in a nightclub district in Bali frequented by Western tourists. Synchronized bomb blasts and subsequent fires in a nightclub district popular with young tourists and backpackers killed approximately 200 and injured some 300, mainly Australians and Indonesians, but also including several Americans as well as Canadians, Europeans, and Japanese. The bombings, the most deadly terrorist attack since the September 11, 2001 attacks in the United States, appeared to mark a shift in JI's strategy; the FBI reported that in early 2002, senior JI leaders—meeting in Thailand—decided to attack "softer targets" in Asia such as tourist sites frequented by Westerners.62 The focus on soft targets was returned to in a second Bali bombing in October 2005. In that attack, at least 20 were killed and over 100 injured, including two Americans and other Westerners, when three suicide bombers attacked restaurants frequented by foreigners.63

The 2002 Bali bombing spurred the Indonesian government to reverse its previous reluctance to investigate JI. In the days after the blasts, senior Indonesian officials acknowledged for the first time that Al Qaeda was operating in Indonesia and was cooperating with JI.64 With the substantial aid of Australian and U.S. investigators, Indonesian police arrested several suspects, including Ali Gufron (also known as Mukhlas), who is thought to be a senior JI commander and an associate of Baasyir. Trials began in the spring and summer of 2003. On August 7, 2003, Islamic militant Amrozi was sentenced to death by an Indonesian court for his involvement in the Bali bombings. The government also announced a series of decrees that strengthen the hand of the government in dealing with terrorism.

Other bombings believed to have been carried out by JI since 2002 include the bombing of the Marriott Hotel in Jakarta in August 2003 that killed more than ten people and injured dozens; the bombing of the Australian Embassy in September 2004, killing 10 and wounding around 200; and the Bali II bombing of October 2005, in which three suicide bombers exploded bombs within minutes of one another in Bali, killing more than 20 people and wounding more than 100. All of the attacks are believed to have been planned by the now deceased Noordin Muhammad Top. Most of the victims have been Indonesians.

Analysts have highlighted the importance of understanding how jihad networks are changing. These networks increasingly depend on personal contacts and are focused on inter-communal strife in the Mulukus and in Poso. Reportedly many of these incidents have involved elements of JI as well as offshoots of Darul Islam and Kompak. This is because many of the militants see these areas as the most likely sites from which an enclave can be carved out where Islamists can live by their interpretation of Islamic principles. This they reportedly believe can then serve as a "building block of an Islamic state."65 The increased militant activity in Maluku and Poso in 2005 appears to be more directly linked to local dynamics, with future objectives at the state and possibly regional level, rather than to global jihad.66

The Trial and Release of Baasyir

The Bali bombing spurred the Indonesian government to arrest Baasyir. He had long been viewed by U.S. officials as directly involved with terrorism, but until the Bali bombing the Indonesian government had not acknowledged his role or arrested him for fear of an anti-government backlash. Although several of those charged with carrying out the Bali attack have implicated Baasyir in the attack, the lack of sufficient evidence led Indonesian authorities to charge him with involvement in past terrorist plots, including an attempt to assassinate Megawati Sukarnoputri when she was Vice-President. Baasyir's highly publicized trial began in the spring of 2003. Baasyir denies leading JI, though he acknowledges training at his Al Mukmin school all of the 13 suspects arrested in Singapore in December 2001.67

On September 3, 2003, an Indonesian court convicted him of plotting to overthrow the Indonesian government. Baasyir was sentenced to four years in jail. Prosecutors had asked for a 15-year sentence. In March 2004, the Indonesian Supreme Court reduced Baasyir's sentence. He was to be released in May 2004, but at the end of April, Indonesian police announced that Baasyir had been declared a suspect in other terrorist attacks, which allowed them to continue his detention. Some prominent Indonesians have said the move came as a result of pressure from the United States and Australia.68

As the trial against Baasyir proceeded it appeared that the prosecution had a relatively weak case. This may have been the result of the prosecution's inability to get key witnesses to testify against Baasyir.69 None of the 32 witnesses for the prosecution directly connected Baasyir with the Bali or Marriott bombings, though some did connect Baasyir to JI training camps in the southern Philippines.70 Only one witness testified that Baasyir was the leader of JI.71

The prosecution called for only a reduced sentence of eight years in jail instead of the death penalty. Baasyir was sentenced to 30 months' imprisonment for conspiracy in the 2002 Bali bombings in April 2004. His sentence was reduced in August 2005 by four months and 15 days. He was released in June 2006, and in December 2006 an Indonesian judge overturned his conviction.

Since his release Bassyir has traveled and preached openly in Indonesia. He has continued to call for the implementation of sharia law, to state that democracy and Islam are incompatible, and to say that Muslims should resist U.S. and Western influence.72 He has also called for Indonesia's anti-terror unit, Detachment 88, to be disbanded claiming that it is a tool of the United States to stigmatize Islam.73 In September 2008, many JI members reportedly joined Baasyir's new organisation Jamaah Ansharud Tauhid (JAT), a radical but above-ground and nonviolent group that rejects democracy and seeks the immediate application of Islamic law.74

U.S.-Indonesia Cooperation

Bilateral relations between the United States and Indonesia have improved dramatically since 2005. Expectations are that they will continue to improve under President Obama, who spent part of his childhood in Indonesia. This improvement in bilateral relations since 2005 was largely the product of a successful democratic process in 2004 that led to the election of President Susilo Bambang Yudhoyono and an increased appreciation of Indonesia's democratic evolution in the United States. This, and the importance of Indonesia to the war against violent Islamic extremists in Southeast Asia and Indonesia's regional geopolitical importance, led the Bush Administration to decide in February 2005 to allow Indonesia to participate in International Military Education and Training (IMET). This was followed by a May 2005 decision to restart non-lethal Foreign Military Sales (FMS) to Indonesia and a November 2005 decision to waive Foreign Military Financing (FMF) restrictions due to U.S. national security concerns.75

The Philippines

The Philippines condemned the September 11, 2001 attacks and offered ports and airports for use by U.S. naval vessels and military aircraft for refueling stops. Philippine President Gloria Macapagal-Arroyo and President Bush agreed on the deployment of U.S. military personnel to the southern Philippines to train and assist the Philippine military against the terrorist Abu Sayyaf group, making the Philippines one of the most extensive examples of U.S. counterterrorism cooperation in Southeast Asia. This agreement was reached under a Visiting Force Agreement that the Philippines and the United States signed in 1999 that provided for the dispatch of U.S. military forces to the Philippines to provide training and other assistance to the Philippine Armed Forces (AFP).76

Abu Sayyaf

Abu Sayyaf is a small, violent, faction-ridden Muslim group that operates in the western fringes of the big island of Mindanao and on the Sulu islands extending from Mindanao. It has a record of killings and kidnappings and has had links with Al Qaeda. Abu Sayyaf kidnapped three American citizens in May 2001. One was beheaded in June 2001. The other two, a missionary couple, were held by Abu Sayyaf until June 2002 when Filipino army rangers encountered the Abu Sayyaf groups holding the couple. In the ensuing clash, the husband and a Filipina female hostage were killed, but the wife was rescued.

Under pressure from U.S.-supported Philippine military operations since 2002, Abu Sayyaf's armed strength has declined from an estimated 1,000 to about 400. It continued to operate in the Sulu islands south of Basilan and on the western Mindanao mainland. It has re-established a small presence on Basilan since 2006. Abu Sayyaf has ties with military factions of the Moro Islamic Liberation Front (MILF) and JI. Two leading JI leaders, Umar Patek and Dulmatin, reportedly are with Abu Sayyaf on the island of Jolo. In the Sulu islands, especially Jolo, it has links with another Muslim groups, the Moro National Liberation Front (MNLF). Abu Sayyaf and JI reportedly engage in joint training with emphasis on training in bomb-making and planning urban bombings.77 By mid-2005, JI personnel reportedly had trained about 60 Abu Sayyaf cadre in bomb assembling and detonations.78 Since 2003, Abu has carried out bombings and plotted bombings in cooperation with JI and the MILF, including bombings in Manila.


The U.S. focus on Abu Sayyaf is complicated by the broader Muslim issue in the southern Philippines, including the existence of a larger insurgent-terrorist group, the Moro Islamic Liberation Front (MILF). The MILF, with an estimated armed strength of 10,000-12,000, broke away from another Muslim group, the Moro National Liberation Front (MNLF) in the late 1970s. Its main political objective has been separation and independence for the Muslim region of the southern Philippines. Evidence, including the testimonies of captured Jemaah Islamiyah leaders, has pointed to strong links between some elements of the MILF and JI, including the continued training of JI terrorists in MILF camps and the planning of terrorist operations. MILF senior leaders have described local commanders as younger and more militant and radical.79 This training appears to be important to Jemaah Islamiyah's ability to replenish its ranks following arrests of nearly 500 cadre in Indonesia, Malaysia, and Singapore.80 The Philippine National Intelligence Coordinating Agency estimated in mid-2009 that there were 30 to 40 JI cadre on Mindanao.81 A stronger collaborative relationship has developed between MILF commands and Abu Sayyaf since 2002, according to Zachary Abuza, a U.S. expert on Islamic terrorism in Southeast Asia.82

The MILF and the Philippines government reached a cease-fire agreement in 2003. A team of international observers led by Malaysia began to monitor the cease-fire in October 2004. However, negotiations for a permanent settlement stalemated over the issue of the MILF's proposal for the establishment of a "Bangsamoro" autonomous state covering much of western Mindanao, the Sulu islands, and part of the island of Palawan. The outlook worsened in April 2008 when Malaysia announced that it would withdraw from the international cease-fire monitoring group. The Malaysian government criticized the Philippine government for lack of flexibility in the negotiations with the MILF.83

In August 2008, the Philippine government and the MILF signed a Memorandum of Agreement laying out a framework for a settlement to end the MILF insurgency and recognition of the ancestral domain of Filipino Muslims. The Memorandum of Agreement provided for the establishment of a Bangsamoro Juridical Entity (BJE), comprising a substantial area of Mindanao. The inclusion of some villages and towns would be determined through plebiscites. The BJE would have an "associative relationship" with the Philippine government, including "shared authority and responsibility." It would be able to create its own government, election system, banking system, schools, judicial system and police and internal security forces. The economic resources of the region would be allocated between the Philippine government and the BJE on a 75-25 percent basis favoring the BJE. The BJE could enter into trade and economic relations with foreign countries and would control the resources of waters extending 15 kilometers from its coast.

Immediately after the conclusion of the Memorandum of Agreement, Christian politicians and elected officials on Mindanao filed a suit with the Philippine Supreme Court, calling for the Court to block the Memorandum. The petitioners claimed that they had not been consulted about the agreement. Resistance to the Memorandum reportedly also came from entrenched political and economic interests on Mindanao, opposition politicians in Manila, and major newspapers. The Supreme Court ruled on October 14, 2008, that the Memorandum of Agreement was unconstitutional in that the "associative relationship" envisaged was illegal in that it implied eventual independence for the BJE.

Renewed fighting between the AFP and the MILF broke out following the collapse of the accord, reportedly resulting in the displacement of over 600,000 villagers and dozens of deaths. Several MILF "rogue" commands attacked Christian villages. The AFP launched operations against these "rogue" groups but not the MILF as a whole. Malaysia withdrew its troops from the International Monitoring Team (IMT), which had been created in 2004 to solidify the 2003 cease-fire. The government and the MILF managed to negotiate a new cease-fire agreement in July 2009. They also agreed in September 2009 on a new round of peace negotiations that would include the establishment of an International Contact Group, made of invited foreign governments, that would act as a "facilitator."84 The MILF argued strongly for the International Contact Group. However, prospects for renewed negotiations are poor in the near to medium term. Philippine presidential elections are scheduled for 2010, placing President Arroyo's administration in a potential lame duck status. Distrust of the MILF, Malaysia's role, and renewed negotiations is strong in the Philippine Congress and the elite media.85

The Philippine Communist Party (CPP)

The CPP, the political head of the New Peoples Army (NPA), also has called for attacks on American targets. The Bush Administration placed the CPP and the NPA on the official U.S. list of terrorist organizations in August 2002. It also pressured the government of the Netherlands to revoke the visa privileges of Communist Party leader, Jose Maria Sison, and other CPP officials who have lived in the Netherlands for a number of years and reportedly direct CPP/NPA operations. In December 2005, the European Union placed the CPP/NPA on its list of terrorist organizations. Recent statements by the Philippine government and the CPP's political front, the National Democratic Front, place NPA armed strength at 5,000-6,000.

U.S. Support for Philippine Military Operations

The Bush Administration has supported the Philippine government's policy of applying military pressure on Abu Sayyaf and seeking a negotiated settlement with the MILF. In 2002, the United States committed nearly 1,300 troops to the southern Philippines to assist the Philippine armed forces (AFP) in operations against Abu Sayyaf on the island of Basilan southwest of Mindanao. In 2005, the United States committed about 450 troops to support two AFP operations. One has focused on Abu Sayyaf in western Mindanao. The second has focused on the Sulu islands southwest of Basilan, especially the island of Jolo, a longtime redoubt of Abu Sayyaf.

The U.S. role in all of these operations is supposed to be non-combat. U.S. forces are known to have fired their weapons on two occasions since 2002.86 The U.S. role has involved the provision of intelligence and communications support of the AFP, including the employment of U.S. P-3 surveillance aircraft; deployment of Navy Seal and Special Operations personnel with AFP ground units; joint training exercises with the AFP, assistance to the AFP in planning operations; and conducting civic action projects with AFP to improve the lives of the local populace and turn it against Abu Sayyaf.87 The U.S. Agency for International Development has concentrated U.S. aid projects on Jolo and neighboring Tawi Tawi island as part of the $260 million in U.S. aid committed to the southern Philippines since 2001.88

U.S. military support reportedly has achieved successes. AFP operations against Abu Sayyaf have become more aggressive and effective on Basilan and Jolo. Abu Sayyaf strength has been eroded to an estimated 200-400, and key commanders have been killed. AFP commanders praised U.S. equipment, U.S. intelligence gathering, and U.S. assistance in planning AFP operations. The U.S. military's civic action projects on Basilan and Jolo (medical treatment, water purification installations, farm markets, renovation of schools) appear to have weakened support for Abu Sayyaf on the islands.89 However, major armed clashes continue on Jolo, and some of these reportedly involved collaboration between Abu Sayyaf and elements of the MNLF.

Filipino leftists groups strongly opposed the presence of the U.S. military, and broader doubts about it began to be expressed in 2009 in reaction to several incidents. On August 21, 2009, Pentagon officials announced that Secretary of Defense Robert Gates had decided to keep the U.S. military contingent of approximately 600 in the Philippines indefinitely. A few days later, a former AFP officer, who had been involved in past joint Philippine-U.S. military operations, charged that U.S. military personnel were "embedded" with AFP combat units on Mindanao and in the Sulu islands and that the U.S. military had established separate U.S. bases in these regions.90 In September 2009, the second known incident of U.S. troops firing their weapons took place when U.S. military personnel on Jolo reacted to a terrorist who threw a grenade at them and a group of Philippine Marines. In September 2009, also, two U.S. Navy Seabees were killed by a roadside bomb on Jolo as they and Philippine Marines were traveling to a village where they were constructing school buildings and artesian wells. The Philippine Senate passed Resolution 1356 expressing the "sense of the Senate" that the Philippine Department of Foreign Affairs should seek to renegotiate the Visiting Forces Agreement (VFA) with the United States and should give notice of termination of the VFA if the United States refused to renegotiate. The resolution asserted that the VFA failed to specify the period of stay of U.S. forces and define specifically the activities U.S. forces could undertake. Several non-government groups petitioned the Philippine Supreme Court to review the constitutionality of the VFA. Officials of the Arroyo Administration defended the VFA and U.S. military assistance to the AFP. AFP commanders declared that U.S. military personnel had rightfully and properly defended themselves in the Jolo firing incident.91 However, the Arroyo Administration announced that its Presidential Commission on the VFA would conduct a review of it and would present recommendations.

In supporting Philippine government-MILF negotiations, the Bush Administration has stated that negotiations are the best means of de-linking the MILF from Jemaah Islamiya and Abu Sayyaf.92 MILF leaders asked the Bush Administration to play a more direct role in its negotiations with the Philippine government.93 The State Department indicated support for the Memorandum of Agreement of August 2008. A group of former U.S. ambassadors to the Philippines wrote in The Wall Street Journal Asia in September 2008 that "the Philippine Supreme Court precipitated a true crisis" when it rejected the Memorandum of Agreement and that "something very much like the recently suspended agreement would have to be part of any future settlement."94


Thailand has endured a persistent separatist insurgency in its majority-Muslim southern provinces, which include the provinces of Yala, Narathiwat, Pattani, and to a lesser extent Songhkla, while dealing with deep political instability in its capital.95 Since January 2004, sectarian violence between insurgents and security forces in the country's majority-Muslim provinces has left over 3,400 people dead, according to press reports.96 The groups that have led this surge in violence are generally poorly understood and their motives are difficult to characterize.

Groups active in the region are inspired by long-held perceptions that the country's ethnic-Thai Buddhist majority mistreats the ethnic-Malay Muslim community. (There are approximately 1.3 million ethnic Malays in Yala, Narathiwat and Pattani, 80% of the population of the provinces, through a small fraction of Thailand's overall population of 65 million.) There is no evidence of a broader anti-Western agenda among the groups active in the region. Most experts believe they are mostly focused on local autonomy. There is also little evidence that foreign jihadi groups are significantly active in southern Thailand, although periodic reports suggest that militants elsewhere in Southeast Asia have used the plight of Thai Muslims as inspiration for their own causes, and have offered occasional material support to groups in southern Thailand.97

Attention in Bangkok has been diverted by deep-set political turmoil since 2006, which has made it difficult for successive Thai governments to forge a coherent strategy for dealing with the Southern insurgency. A bloodless military coup in September 2006 ousted the democratically-elected Prime Minister Thaksin Shinawatra, whose government had pursued an aggressive campaign against militants in the South. Thaksin was followed by a military-led interim government which took control for 15 months. A civilian government took power after elections were held in December 2007, and it was in turn replaced in December 2008 after its leader was impeached. The current coalition government is led by Abhisit Vejjajiva and the Democrat Party. The successive administrations have taken somewhat different approaches to curbing the violence in the south, but none appear to have found a way to resolve the ongoing insurgency.

Southern Insurgency

The southern region of Thailand has a history of separatist violence dating to the early 20th Century, though the major movements were thought to have died out in the early 1990s. Thai Muslims have long expressed grievances for being marginalized and discriminated against, and the area has lagged behind the rest of Thailand in economic development. The recent death toll of over 3,400 includes suspected insurgents killed by security forces, as well as victims of the insurgents. This includes both Buddhist Thais, particularly monks and teachers, and local Muslims. According to the International Crisis Group, a significant majority of those killed have been Muslims.98

After a series of apparently coordinated attacks by the insurgents in early 2004, the central government declared martial law in the region. Moreover, a pattern of insurgent attacks—targeted shootings or small bombs that claim a few victims at a time and counter-attacks by the security forces—has developed. The pattern crystallized into two major outbreaks of violence in 2004: on April 28, Thai soldiers killed 108 insurgents, including 34 lightly armed gunmen in a historic mosque, after they attempted to storm several military and police outposts in coordinated attacks; and on October 25, 84 local Muslims were killed: 6 shot during an erupting demonstration at the Tak Bai police station and 78 apparently asphyxiated from being piled into trucks after their arrest. The insurgents retaliated with killings, including beheadings, following the Tak Bai incident. Video of the incident has reportedly been used by rebel groups as a recruiting tool.99

Approaches of Recent Governments

The Thaksin government's handling of the violence was widely criticized as ineffective and inflammatory. Critics charged that the Thaksin Administration's aggressive approaches led to atrocities including the 2004 Tak Bai killings, that it never put forth a sustained strategy to define and address the problem, that it repeatedly and arbitrarily shuffled leadership positions of those charged with overseeing the region, and that it failed to implement adequate coordination between the many security and intelligence services on the ground.

After Thaksin's ouster, interim Prime Minister Surayud Chulanont took a more conciliatory approach by publicly apologizing to Muslim leaders for past government policies in the South and resurrecting a civilian agency responsible for improving relations between the security forces, the government, and southern Muslims that Thaksin had abolished. General Sonthi Boonyaratglin, leader of the coup and the first Muslim commander of the Army, advocated negotiations with the separatist groups as opposed to the more confrontational strategy pursed by Thaksin.

The following government, led by Thaksin ally Samak Sundaravej, was consumed with its own survival in the face of massive protests and counter-protests by its opponents and loyalists in Bangkok. Observers said it largely left management of the Southern conflict to the military. There was a lessening of violence during 2008, but some analysts said that a younger generation of more radicalized insurgents resisted the more conciliatory approach of the new leadership in Bangkok.

Current Government's Approach

The current government, led by Prime Minister Abhisit Vejjajiva, has been faced with a renewed rise in violence in 2009.100 Abhisit has pledged to take back some level of policy from the military, and on August 23, 2009, announced that the Southern Border Provinces Administrative Center, which coordinates Thai government activity in the region, would report to the Prime Minister rather than the military. Abhisit has made several trips to the South, and announced plans to visit the region with Malaysian Prime Minister Najib Razak by the end of 2009.

The region remains under martial law, which allows security forces to arrest suspects without warrants and detain them for up to 30 days. Since June 2007, a more concentrated counter-insurgency campaign know as "Operation Southern Protection" has led to far more arrests, but many analysts see the mass arrests as fueling local resentment. Observers note an increase in more lethal and bold attacks, including a March 2008 car bombing of a prominent hotel in Pattani that is known for hosting official delegations.101 Human rights groups have continued to criticize the military for its mistreatment of Muslim suspects; in March 2008, Human Rights Watch accused the army of torturing an arrested Muslim cleric who later died in police custody.102

Close observers note that attacks have become more provocative, more deaths are caused by increasingly powerful explosions, and the insurgents have directed more attacks at economic targets, particularly those owned by ethnic Chinese. Some analysts describe a movement increasingly driven by an Islamist agenda: the insurgents appear intent on driving a harsher ideological line and labeling conciliatory Muslims as collaborators. Because of the repeated attacks on state-run schools, many citizens have chosen to send their children to private Islamic schools. The insurgents' village-level network has expanded, perhaps driving more local support.103 As the attacks have become more sophisticated and coordinated, a climate of fear has developed and division along religious lines has accelerated. According to some reports, 15% of the Buddhist population has left the region.104

Little Evidence of Transnational Elements

Most regional observers stress that there is no convincing evidence to date of serious Jemaah Islamiyah (JI) involvement in the attacks in the southern provinces, and that the overall long-term goal of the movement in the south remains the creation of an independent state with Islamic governance. Many experts characterize the movement as a confluence of different groups: local separatists, Islamic radicals, organized crime, and corrupt police forces. They stress, however, that sectarian violence involving local Muslim grievances provides a ripe environment for foreign groups to become more engaged in the struggle. Such experts have warned that outside groups, including JI and other militant Indonesia-based groups, may attempt to exploit public outrage with events like the October 2004 Tak Bai incidents to forge alliances between local separatists and regional Islamic militants. Some of the older insurgent organizations earlier were linked to JI, have reportedly received financial support from foreign Islamic groups, and have leaders who have trained in camps in Libya and Afghanistan. Despite these links, foreign elements apparently have not engaged significantly in the violence.

Leadership of Insurgency Unclear

Identifying the groups directing the insurgency has been challenging, but most analysis suggests that there is no single organization with authority over the others. Some reports suggest that the Barisan Revolusi Nasional-Coordinate (BRN-C) has coordinated other groups that operate largely autonomously. Other actors include older Islamist separatist groups such as the Pattani United Liberation Organization (Pulo)—which has a higher public profile internationally than BRN-C, but which is widely considered to have less influence on the ground—and Gerakan Mujahideen Islam Pattani (GMIP). In April 2008, a Pulo website claimed that its members were committed to resolving the violence through a dialogue with the Thai government, but neither the central government nor the other groups followed suit. An organization called Bersatu at one point claimed to be an umbrella grouping for all the insurgent factions, but appears to have very limited authority over the disparate networks. The failure of the Thai government to establish an authority with whom to negotiate limits its ability to resolve the conflict peacefully.

U.S.-Thai Cooperation

Part of the U.S. concern about Thailand's vulnerability to international terrorism stems from Thailand's relatively lax border controls and tourist-friendly visa requirements. Confessions of detained Al Qaeda and JI suspects indicate that the groups have used Thailand as a base for holding meetings, setting up escape routes, acquiring arms, and laundering money. There have been indications of JI presence in Thailand, particularly given the 2003 arrests of Hambali, a radical figure with suspected ties to Al Qaeda, and of three Islamic leaders suspected of planning to attack foreign embassies and tourist destinations. In January 2002, Hambali is reported to have convened a meeting of JI's operatives in southern Thailand at which the group agreed to attack "softer" targets. A number of Al Qaeda and JI figures, including convicted World Trade Center bomber Ramzi Yousef, have fled to Thailand to escape arrest in other Southeast Asian countries.

Thailand and the United States have close anti-terrorism cooperation, institutionalized in the joint Counter Terrorism Intelligence Center (CTIC), which was reportedly established in early 2001 to provide better coordination among Thailand's three main security agencies. The U.S. Central Intelligence Agency reportedly shares facilities and information daily in one of the closest bilateral intelligence relationships in the region. According to press reports, the CTIC took the lead in capturing Hambali and also has captured a number of other suspected JI operatives, acting on CIA intelligence. Thailand also reportedly provided a black site where U.S. CIA officials were allowed to secretly hold suspected terrorists.105 According to press reports, two major Al Qaeda figures captured in Pakistan were flown to Thailand for interrogation by U.S. officials in 2002.

It is unclear to what extent U.S.-Thai counterterrorism cooperation was affected by the U.S. response to the military coup in September 2006. Unspecified counterterrorism funds appropriated under Section 1206 of the National Defense Authorization Act for FY2006 were suspended, but other programs "deemed to be in the U.S. interest" continued, according to the U.S. State Department. Regardless, the State Department certified that Thailand had restored a democratically elected government in February 2008, removing legal restrictions to providing assistance to Thailand, which continues under the Abhisit government.


Unlike many of its neighbors in Southeast Asia, Malaysia has no indigenous separatist groups or insurgents that are generally viewed as engaging in terrorist activities. The purported terrorist groups that do remain in Malaysia are generally external in nature, comparatively small and relatively inactive. Following the events of September 11, 2001, Malaysia was briefly considered a "hot spot" for global terrorism because some of plotters of the attacks reportedly met in Kuala Lumpur.

Because Malaysia views itself as a prime example of a moderate Muslim nation, it believes it has a better understanding of the causes of and solutions for terrorism than Western nations. During the administrations of former Prime Ministers Mahathir Mohammed and Abdullah Badawi, Malaysia maintained that U.S. anti-terrorism policies and strategies were leading to the growth—not the decline—in the membership and popular support for so-called "terrorist groups." Instead, Malaysia advocated an approach that focused on combating what it sees as root causes of terrorism, such as poverty and the denial of human rights.

Despite these sharp differences in their policies and strategies, Malaysia has historically been supportive of specific U.S. counter-terrorism programs and initiatives in Southeast Asia. However, some aspects of Malaysia's domestic counter-terrorism programs have been sharply criticized for curtaining civil liberties and providing the Malaysian government with tools to suppress political opposition. The perceived weakness of the Malaysia's current leadership following the 2008 elections is contributing to renewed calls for the repeal or reform of Malaysia's anti-terrorism laws.106

Recent Events

Like the United States, a new administration took office in Malaysia in 2009. On April 3, 2009, Mohd Najib bin Tun Abdul Razak was sworn in as Prime Minister of Malaysia. Prime Minister Najib had served as Defense Minister and Finance Minister during the previous Badawi administration. As a senior minister of the Badawi administration, Prime Minister Najib expressed support for Badawi's critical comments about U.S. policy on terrorism. It is unclear if his critical stance will continue now that he is Prime Minister and the Obama administration has taken office in the United States. In addition, there are pressures mounting within Malaysia for the reexamination of the nation's existing anti-terrorism laws, particularly its Internal Security Act (ISA).

Since the onset of the global economic crisis, Malaysia has reiterated the link between economic conditions and extremism. During the 8th Association of Southeast Asian Nations (ASEAN) Senior Officials Meeting on Transnational Crime (SOMTC) in June 2008, Malaysia's Home Minister Syed Hamid Albar linked the declining global economic situation to a potential rise in terrorism and other forms of crime.107 The Home Minister's views were reflected in the comments of then Prime Minister Badawi during the July 2008 D8 meeting in Kuala Lumpur.108

The issue of terrorism in Malaysia in 2009 arose in two distinct areas. First, the July 17, 2009 hotel bombings in Jakarta were widely associated with Noordin Top, a Malaysian national with a history of involvement with terrorist activities (see "The July 2009 Jakarta Hotel Bombings" above). Second, there is mounting pressure within Malaysia for major changes in its anti-terrorism laws, particularly its Internal Security Act.

A Muslim Voice of Moderation

Malaysia is an ethnically-diverse, predominantly Islamic nation with large Chinese and Indian minorities. From its beginnings, Malaysia has sought to balance its identity as an Islamic nation with its culturally diverse population. Ex-Prime Minister Badawi once stated that "we are responsible for ensuring that the culture of extremism and violent acts in the name of Islam does not happen in Malaysia."109 In recent years, the Malaysian government tried to place itself at the center of the debate within the Islamic community at fora such as the Organization of the Islamic Conference (OIC) on what Malaysia sees at the true values of Islam and Islam's history of religious and cultural tolerance. Prime Minister Najib has offered a new vision of a harmonious, multicultural Malaysia under the slogan "1Malaysia." According to its official web page (http://www.1malaysia.com.my), "1Malaysia" is "the idea that our differences in race and religion are what make our country distinct."

The Malaysian government was highly critical of the past U.S. policy on terrorism. Malaysia views the U.S. "invasions" of Afghanistan and Iraq, as well as the continuing "occupation" of Iraq, as contributing to the growth of membership and popular support of terrorist groups. In addition, past Malaysian governments have viewed the "pro-Israel" bias of the United States as a barrier to the resolution of the Palestinian problem and another source of rising support for terrorist groups. Also, Malaysia has been critical of the perceived U.S. tendency to "stereotype" terrorism as being a problem peculiar to Islam, contributing to a rise in anti-Islam rhetoric.110 During the June 2008 gathering of the Organization of the Islamic Conference, Prime Minister Badawi reportedly stated, "This biased view (of Islam) in the West persists, and, I must admit, it is not helped by the misguided actions of a discredited few from the Muslim side."111 It is unclear if the new Najib Administration will continue the past criticism of U.S. policy.

Maritime Concerns

The threat of piracy and seaborne terrorism in the region, particularly in the vital Straits of Malacca between Malaysia, Singapore, and Indonesia, continues to be a cause for concern. This is due to the strategic importance of the sea lanes to international trade and its vulnerability to attacks against shipping. Indonesia, Malaysia, Singapore, and Thailand have made progress in addressing potential terrorist and pirate threats to maritime shipping lanes in the Straits of Malacca by agreeing on operating procedures that will allow patrols of each state to enter into the territorial waters of others when in pursuit of pirates or terrorists.112

There are also allegations that Malaysia businesses are one of the major conduits for illegal shipments of arms to terrorist organizations in Iran. Recent reports state that unnamed U.S. officials assert that U.S. military equipment and technology are being shipped to Iran via Malaysian middlemen. Malaysia's Home Minister Hishammuddin Hussein has dismissed these claims, stating, "We would know if there are any smuggling activities going on as we are constantly fighting against borderless crimes."113 Minister Hussein has called upon U.S. officials to provide evidence of illegal arms shipments via Malaysia.

Terrorism and Counter-Terrorism in Malaysia

The level of terrorist activity in Malaysia is considered comparatively low to other Southeast Asian nations. The Malaysian government maintains that its strict laws and police activity undermined the previously existing networks of terrorism in Malaysia and continue to prove to be an effective deterrent to extremism. Critics of Malaysia's anti-terrorism laws claim that the laws are no longer necessary, and are primarily being used to suppress political opposition to Malaysia's ruling Barisan Nasional (BN) political coalition.

Terrorist Groups in Malaysia

Beside Al Qaeda and the JI, other extremist groups that at one time were reportedly active in Malaysia include the Abu Sayyaf Group and the Kampulan Mujiheddin Malaysia (KMM). The Abu Sayyaf Group, which abducted tourists at a Malaysian resort in 2000 (using speedboats to cross the border from bases in the Philippines), reportedly split from the much larger Moro National Liberation Front in the early 1990s under the leadership of Abdurajak Abubakar Janjalani. The KMM is a small, militant group calling for the overthrow of the Malaysian government and the creation of a pan-Islamic state encompassing Indonesia, Malaysia, and the southern Philippines. Founded in 1995, the group is estimated by Malaysian authorities to have fewer than 100 members. According to Singaporean and Malaysian authorities, the KMM has close links to JI and radical Islamist groups in the Malukus and the Philippines.

The Malaysian government has also made assertions that Malaysia's Hindu Rights Action Force (HINDRAF) has associations with terrorist groups, and has arrested some of its leaders using its anti-terrorism laws. On December 12, 2007, five HINDRAF leaders were detained under the provisions of the ISA, claiming that the organization has ties to the LTTE. HINDRAF has reportedly denied it has any links to the LTTE or other terrorist groups.114 In August 2009, P. Uthayakumar, a legal advisor to HINDRAF and a leader of the new Human Rights Party, was charged with sedition for writing an open letter to British Prime Minister [author name scrubbed] criticizing Malaysia's ISA. Uthayakumar's trial began on September 28, 2009.

Malaysia's Counter-Terrorism Efforts and Their Critics

Malaysia relies on a number of laws for its counter-terrorism efforts. The most prominent and controversial law is the Internal Security Act (ISA). Originally passed in 1960, the ISA allows for the arrest and detention of people without charge for up to two years if the Home Minister determines that the detainees pose a threat to national security. Other counter-terrorism laws went into effect in March 2007 that provide for the forfeiture of terrorist-related assets, allow for the prosecution of those who materially support terrorists, and expand surveillance of suspects.115 At present, there are only nine people being detained under the ISA. The most prominent detainee is Mas Selamat Kastari, who escaped detention in Singapore, but was subsequently captured in Malaysia.

In August 2009, information about a Malaysian plan to develop an Internet filtering system to combat pornography, gambling, and terrorism was leaked to the press, raising concerns about censorship and potential abuse for political purposes. It was alleged that the Ministry of Communications and Culture was developing a filtering system for the Internet that would block access to selected web pages. After protests from a number of non-government organizations, the media, and some members of Malaysia's opposition parties, the government announced it was formally dropping the project.

During the last two years, pressure to repeal or reform of the ISA have grown. Two of Malaysia's leading opposition political parties—the Parti Islam Se-Malaysia (PAS) and the Parti Leadilan Rakyat (PKR)—have stated the ISA should be repealed. In June 2008, the Malaysian Bar Council called on the Malaysian government to abolish the ISA following a court decision that an activist's arrest and detention was clearly done for political reasons, and were not based on any threat to national security.116 Malaysia's anti-ISA coalition, the Gerakan Manuhkan ISA (GMI), stated in December 2008 that the government's claim that the ISA has "protected the country from terrorism" was "baseless and unconvincing," and "in reality, the ISA itself has served as an instrument of terror of the State…"117 On August 1, 2009, about 40,000-50,000 people participated in an anti-ISA rally in Kuala Lumpur. The Parti Gerakan Rakyat Malaysia (Gerakan), a member of the ruling BN coalition, reportedly supports reforming the ISA to narrow its scope to cover only matters related to terrorism.118

Despite the growing opposition to the ISA, the Malaysian government sees the law as playing an important role in its anti-terrorism efforts, often comparing it to the U.S. PATRIOT Act and the United Kingdom's Anti-Terrorism Act. However, it has been reported that Najib administration is considering making amendments to the ISA and the Police Act.119 Deputy Home Minister Wira Abu Seman Yusop has said that a review paper of the ISA may be presented to Malaysia's Parliament as early as October 2009.120

U.S.-Malaysia Counter-Terrorism Cooperation

The United States and Malaysia signed a Memorandum of Understanding (MOU) on counter-terrorism in May 2002. The text of that document became the basis for a subsequent declaration on counterterrorism that the United States and ASEAN signed at the August 2002 ASEAN Regional Forum (ARF) meeting.121 In January 2009, a Mutual Legal Assistance Treaty (MLAT) between Malaysia and the United States came into force. The MLAT allows authorities from each nation to assist each other in criminal investigations and proceedings. The MLAT is not an extradition treaty.


Shortly after the September 11, 2001 attacks in the United States, Singaporean authorities launched aggressive operations to counter terrorist activities.122 Under its Internal Security Act, Singapore has arrested dozens of suspected Islamic militants, many of whom are alleged to be members or sympathizers of JI. In 2002, Singaporean authorities reportedly uncovered a JI plot to bomb the U.S. Embassy and other western targets in Singapore. Authorities claim that many of the suspects have links to the Philippines-based Moro Islamic Liberation Front (MILF).

Despite its strong counter-terrorism record, Singapore was embarrassed by the February 2008 high-profile prison escape of Mas Selamat bin Kastari, the alleged head of JI in Singapore. Mas Selamat was accused of plotting the embassy bombing. A large scale manhunt failed to find him in the ensuing months, but he was apprehended in April 2009 in Malaysia, where he remains in detention under Malaysia's Internal Security Act. A Singapore government report issued two months after the escape concluded that there had been no inside cooperation in Mas Selamat's escape from the tightly-guarded Whitley Detention Center.

U.S.-Singapore Cooperation

The Joint Counter Terrorism Center (JCTC) coordinates the multiple agencies and departments of the Singaporean government that deal with terrorism, including the intelligence agencies. Since 9/11, Singapore has increased intelligence cooperation with regional countries and the United States. Singaporean authorities have shared information gathered from suspected militants held under the Internal Security Act with U.S. officials, reportedly providing detailed insights into JI and Al Qaeda's structure, methods, and recruiting strategies.

Singapore was a founding member of the Proliferation Security Initiative (PSI), a program that aims to interdict shipments of weapons of mass destruction-related materials, and was the first Asian country to join the Container Security Initiative (CSI), a series of bilateral, reciprocal agreements that allow U.S. Customs and Border Patrol officials to pre-screen U.S.-bound containers. Singapore has led other littoral states in Southeast Asia to jointly protect the critical shipping lanes of the Straits of Malacca from piracy or terrorist attacks.

Enhanced Homeland Security

Singaporean officials maintain that important port facilities and other major targets remain vulnerable and have stepped up protection of these and other critical infrastructure. Measures include camera surveillance of water and power facilities, enhanced security at embassies and prominent public areas, and the deployment of armed personnel at a major petrochemical hub. Singapore has revamped its national security bureaucracy and instituted a "Total Defense" campaign, which calls on all Singaporeans to participate in the national defense. The government intends to psychologically prepare its public for an attack by framing the question of a terrorist attack as "when, not if." A large-scale anti-terrorism exercise in June 2005 involved over 1,000 citizens and public officials and Singapore's public transit systems. The regulation of people and goods across Singapore's borders has been intensified through the merging of the border control functions of the customs and immigration services. To strengthen border security, Singapore has introduced a biometric passport holding a chip that provides the owner's facial and fingerprint identification information. Singapore instituted a Strategic Goods Control (SGC) system that aims to prevent the proliferation of weapons of mass destruction, and is active in international fora that focus on export control regimes, including the Export Control and Related Border Security Assurance (EXBS) program organized by the U.S. Department of State.

Figure 1. Southeast Asia

Figure 2. Indonesia

Figure 3. Malaysia and Singapore

Figure 4. The Philippines

Figure 5. Thailand

Author Contact Information

[author name scrubbed], Coordinator, Specialist in Asian Affairs ([email address scrubbed], [phone number scrubbed])
[author name scrubbed], Specialist in Asian Affairs ([email address scrubbed], [phone number scrubbed])
[author name scrubbed], Section Research Manager ([email address scrubbed], [phone number scrubbed])
[author name scrubbed], Specialist in Asian Affairs ([email address scrubbed], [phone number scrubbed])
[author name scrubbed], Analyst in Asian Trade and Finance ([email address scrubbed], [phone number scrubbed])



 For the purposes of this report, Islamic refers to that which pertains to Islam in general while the term Islamist connotes a concept that advocates a more strict interpretation of Islam and a willingness to push a political and social agenda to implement Islamic law. Distinctions are also drawn between those radicals and extremists who would advocate an Islamist agenda through the political process and those terrorists and militants who would also use violence, or the threat of violence, to promote such a cause.


Daljit Singh,"The Terrorist Threat in Southeast Asia," in Russell Heng and Denis Hew, eds., Regional Outlook, 2003-2004 (Singapore: Institute of Southeast Asian Studies, 2003).


Filipino police discovered the Bojinka plot, which was in the final stages, in January 1995 only because a fire broke out in Yousef's apartment, filling it with poisonous gas from the bomb-making chemicals. Yousef fled to Malaysia, was arrested in Pakistan, and extradited to the United States, where he was sentenced to life imprisonment for his role in the 1993 bombing and the Bojinka plot. See The 9/11 Commission Report, pp. 147-148.


For examples of how the September 11 plot organizers traveled relatively freely throughout Southeast Asia to hold meetings and observe flight and airline employees' patterns, see The 9/11 Commission Report, pp. 156-160.


Report to the UN Security Council by the Security Council Monitoring Group, '1267' Committee, Security Council Report S/2003/669, July 7, 2003, p. 15.


Zachary Abuza, "Terrorism in Southeast Asia," in Strategic Asia 2002-2003 (Seattle, WA: National Bureau of Asian Research, 2003).


Zachary Abuza, Militant Islam in Southeast Asia: Crucible of Terror (Boulder: Lynne Rienner Publishers, 2003).


"Southeast Asia," Jane's Sentinel Security Assessment, March 5, 2008; International Crisis Group, "Indonesia: Tackling Radicalism in Poso," Policy Briefing, Asia Briefing N°75, 22 January 22, 2008; Eric Schmitt, "Southeast Asia Sees Gains against Insurgencies," International Herald Tribune, June 9, 2008; Greg Sheridan, "Jakarta's Terrorist Rehab," The Australian, May 31, 2008.


Indonesia: The Hotel Bombings, International Crisis Group, Policy Briefing, Asia Briefing N°94, July 24, 2009.


For more information on Indonesia see CRS Report RL32394, Indonesia: Domestic Politics, Strategic Dynamics, and American Interests, by [author name scrubbed].


Sidney Jones, "Indonesia Backgrounder: Jihad in Central Sulawesi," International Crisis Group Report No74, February 3, 2004.


Zachary Abuza, "Funding Terrorism in Southeast Asia: The Financial Network of Al Qaeda and Jemaah Islamiyah," NBR Analysis, December 2003, pp. 11-12; The 9/11 Commission Report, pp. 150-152.


Eric Schmitt, "Southeast Asia Sees Gains against Insurgencies," International Herald Tribune, June 9, 2008.


Sidney Jones, "Jemaah Islamiyah in South East Asia: Damaged but Still Dangerous," International Crisis Group Report No 63, August 26, 2003, p. 1; Abuza, "Funding Terrorism in Southeast Asia," p. 9.


The 9/11 Commission Report, p. 151. Yazid Sufaat is the individual JI sent to Kandahar.


Al Qaeda and JI leaders met in Southeast Asia for at least two critical meetings: One in January 2000 in Kuala Lumpur, during which plans for the attack on the USS Cole and the September 11 hijackings were discussed. The other occurred in Bangkok in January 2002, during which an Al Qaeda representative reportedly sat in on the planning of the Bali bombings.


The 9/11 Commission Report, p. 151.


Sidney Jones, "The Changing Nature of Jemaah Islamiya," Australian Journal of International Affairs, June 2005.


Zachary Abuza, "The War on Terrorism in Southeast Asia," in Strategic Asia 2003-04, (Seattle, WA: National Bureau of Asian Research, 2003), p. 333; Jones, "Jemaah Islamiyah in South East Asia," p. ii.


Jones, "Jemaah Islamiyah in South East Asia," pp. 27-28.


Jones, "The Changing Nature of Jemaah Islamiya," p. 170.


"Singapore Arrests Fugitive JI Suspect," Jane's Country Risk Daily Report, May 8, 2009; Indonesia: The Hotel Bombings, International Crisis Group, Policy Briefing, Asia Briefing N°94, July 24, 2009.


Sidney Jones, "Noordin's Dangerous Liaisons," Tempo, August 9, 2009.


Jones, "Jihad in Central Sulawesi," pp. 24-25. The 9/11 Commission Report (note 26 on p.490) notes that during his interrogation, Khalid Sheikh Mohammed said that Baasyir criticized Hambali for focusing too heavily on Al Qaeda's broader, global agenda at the expense of accomplishing JI's aims in Indonesia and Malaysia.


Jones, "The Changing Nature of Jemaah Islamiya," pp. 171-172.


International Crisis Group, Jihadism in Indonesia, Asia Report 127, January 24, 2007.


Romesh Ratnesar, "Confessions of an Al-Qaeda Terrorist," Time, September 23, 2002.


Eric Schmidt and Time Golden, "Details Emerge on a Brazen Escape in Afghanistan," New York Times, December 4, 2005; "Profile: Omar al-Farouq," BBC News, September 26, 2006.


Indonesia: The Hotel Bombings, International Crisis Group, Policy Briefing, Asia Briefing N°94, July 24, 2009; August 2009 e-mail correspondence with terrorism expert Zachary Abuza.


"Noordin the Key in Indonesian Terrorism Raids," Jane's Intelligence Weekly, August 17, 2009.


David Montero, "Indonesia: How Will it Adapt Counterterrorism Strategy?" The Christian Science Monitor, August 19, 2009.


Indonesia: The Hotel Bombings, International Crisis Group, Policy Briefing, Asia Briefing N°94, July 24, 2009.


Sydney Jones, "Noordin's Dangerous Liaiasons," Tempo, August 9, 2009.


Presi Mandari, "Indonesian Bomb Suspect was Al-Qaeda Member: Police," Agence France Presse, August 27, 2009.


Tom Wright, "Hidden Links Bolster Region's Militants," The Wall Street Journal, August 31, 2009.


Tanja Vestergaard, "U.S. Drops Indonesia Travel Warning as Security Situation Improves," Global Insight, May 26, 2008.


"Indonesia Arrests Alleged Bali Bomb Plotter," Agence France Presse, May 5, 2008.


Hamish McDonald, "Fighting Terrorism with Smart Weaponry," The Sydney Morning Herald, May 31, 2008.


Greg Sheridan, "Jakarta's Terrorist Rehab," The Australian, May 31, 2008.


"United States/Indonesia: US, Indonesia Combine Efforts to Fight Transnational Crime, Terrorism," Thai News Service, June 11, 2008.


Eric Schmitt, "Southeast Asia Sees Gains Against Insurgencies Fighting Terrorism," The New York Times, June 9, 2008.


"Australian PM in Indonesia for Talks on Security, Environment," Voice of America, June 13, 2008.


"Radical Islam Regeneration Remains Risk in Indonesia," Reuters, August 11, 2009.


Peter Gelling and Mark McDonald, "Indonesian Police Kill Alleged Terror Mastermind," The New York Times, September 18, 2009.


"Letter Found on Top's laptop Implicates Jibril, States Jaelani Recruited by Al Qaeda in Yemen," OSC, September 29, 2009.


"Indonesian Terror Recruiter Syaifudin Likely Successor to Noordin," OSC, September 25, 2009.


Brian Padden, "Indonesia's Plan to Strengthen Anti-Terror Laws Worries Human Rights Advocates," Voice of America, September 10, 2009.


Aubrey Belford, "Indonesia's Tough Anti-terror Plan Under Fire," Agence France Presse, September 7, 2009.


"Yudoyono Signals Intent to Use Special Forces to Combat Terrorism," OSC, September 12, 2009.


"Indonesia Jails Leaders of 'Terrorist' JI," SBS News, April 22, 2008.


Tanja Vestergaard, "Leaders of Indonesia's Terrorist Group JI Handed 15-Year Sentences," Global Insight, April 22, 2008.


Stephen Fitzpatrick, "We'll Wage War: Muslim Hardliners," The Australian, June 3, 2008.


Julia Suryakusuma, "Zero Tolerance for Bullies and Thugs," The Straits Times, June 12, 2008.


"Indonesia: Communal Tensions in Papua," International Crisis Report No 154, June 16, 2008.


"Indonesia's president Claims Victory in war Against Terror," DowJones Newswire, August 16, 2007.


"Dujana Admits Bakar was JI Spiritual Leader," SBS, June 27, 2007.


Stephen Coates, "SE Terror Groups Pose 'Very Real' Threat: Think Tank," Agence France Presse, June 25, 2008.


Richard Paddock, "Indonesia Presses U.S. to Stop Bombing Asia," Los Angeles Times, November 2, 2001.


"Al-Qaida Planned Indonesia Attack," Associated Press, January 23, 2002. This report cites Indonesian military sources and western intelligence sources that the Indonesian army committed at least $9.3 million to finance Laskar Jihad.


"Support Declines Among Muslims for Violent Defense of Islam," Radio Free Europe, July 26, 2007.


Mark Forbes, "JI Openly Recruits as Leaders Quizzed," The Age, June 23, 2007.


Jay Solomon and James Hookway, "Bali Bomb Suspect Used Thailand as Staging Area," The Wall Street Journal, November 7, 2002.


R. Pura and L. Lopez, "Bali Blast Signals Militants Rebirth," The Wall Street Journal, October 3, 2005.


Ellen Nakashima and Alan Sipress, "Al Qaeda Linked to Blast by Official," Washington Post, October 15, 2002.


"Weakening Indonesia's Mujahidin Networks: Lessons from Maluku and Poso," International Crisis Group, October 13, 2005.


Sidney Jones, "Asking the Right Questions to Fight Terror," The Jakarta Post, January 9, 2006.


Abuza, "Tentacles of Terror," p. 72.


Raymond Bonner, "U.S. Pressure to Hold Militant Sets Off Outcry in Indonesia," New York Times, April 20, 2004.


"Bashir: A Strong Chance to walk Free," Australian Associated Press, February 9, 2005.


Sian Powell, "Call for Baasyir Jail Term," The Australian, February 9, 2005.


"Indonesian Prosecutors Ask for Eight-Year Jail Sentence for Bashir," Voice of America, February 8, 2005.


See, for instance, Michael Sheridan, "Bali Terror Chief's New Mission," The Sunday Times, August 2006.


Mark Forbes, "West Funds Elite Unit to Destroy Islam," The Sydney Morning Herald, June 27, 2007.


; Indonesia: The Hotel Bombings, International Crisis Group, Policy Briefing, Asia Briefing N°94, July 24, 2009.


State Department, Office of the Spokesman, Washington, DC, "Taken Question at Daily Press Briefing," January 4, 2006. Eric John, "U.S. and RI: A Strategic Partnership," The Jakarta Post, January 3, 2006.


For further information, see CRS Report RL33233, The Republic of the Philippines: Background and U.S. Relations, by [author name scrubbed] and [author name scrubbed]; and CRS Report RL31265, Abu Sayyaf: Target of Philippine-U.S. Anti-Terrorism Cooperation, by [author name scrubbed].


Abuza, Zachary. Balik-Terrorism: The Return of the Abu Sayyaf. Carlisle, U.S. Army War College, 2005, p. 27.


Mogato, Manny. "Philippine rebels linking up with foreign jihadists." Reuters News, August 21, 2005. Del Puerto, Luige A., "PNP [Philippine National Police]: Alliance of JI, RP terrorists strong." Philippine Daily Inquirer (internet version), November 20, 2005.


"Philippine Muslim rebel leader says last chance for peace," Agence France Presse, September 19, 2009.


John McBeth, "Across Borders," Far Eastern Economic Review, July 22, 2004. p. 27.


"Noordin's death a blow to Philippine militants: rebels, analyst," Agence France Presse, September 18, 2009.


Abuza, Balik-Terrorism: The Return of the Abu Sayyaf, op. cit., pp. 14-19, 22-24.


Patricio Diaz, "Behind IMT pull-out: fingerpointing," MindaNews (internet), May 19, 2008. Al Jacinto, "Stalled GRP-MILF peace talks; MILF: we stand firm on self-determination," Manila Times (internet version), May 4, 2008.


"Philippines agrees to peace brokers in Muslim conflict: govt," Agence France Presse, September 16, 2009.


Carolyn O. Arguillas, "Biazon committee to ask GRP panel on Malaysia's continued facilitation," MindaNews (internet), September 17, 2009. Roldolfo Biazon heads the Defense Committee of the Philippine Senate.


Julie Alipala, "RP confirms US soldiers fired guns in Jolo," Philippine Daily Inquirer (internet), September 19, 2009.


Raymond Bonner and Carlos Conde, "U.S. and Philippines join forces to pursue terrorist leader," New York Times, July 23, 2005, p. A4. James Hookway, "Terror fight scores in Philippines," Wall Street Journal Asia, June 20, 2007, p. 1. Roland Ramos and Inday Espina-Varona, "Expanded (old) war theater, Philippine Graphic," November 12, 2007, p. 14-18.


Fabio Scarpello, "U.S. diplomat meets Philippines rebels amid ongoing controversy over U.S. presence," AdnKronos International, February 28, 2008.


Simon Montlake, "U.S. troops in Philippines defy old stereotype," Christian Science Monitor, March 1, 2007, p. 7. Al Jacinto, "U.S., Filipino troops go on charm offensive," Manila Times (internet version), September 10, 2007.


Katherine Evangelista, "US troops join combat: ex-RP Navy exec," Philippine Daily Inquirer (internet), August 27, 2009.


Tarra Quismundo, "Shooting by American troops lawful: military," Philippine Daily Inquirer (internet), September 20, 2009.


Asia Security Monitor No. 147, November 2005. "U.S. says peace deal in Manila may pressure JI," Reuters News, October 22, 2005.


William M. Esposo, "Who is the US supporting in the Mindanao war?" Philippine Star (internet), August 19, 2007.


Stephen Bosworth, et al., Fixing Mindanao, Wall Street Journal Asia, September 30, 2008, p. 16.


For more information on political developments in Thailand, see CRS Report RL32593, Thailand: Background and U.S. Relations, by [author name scrubbed].


Internatonal Crisis Group, Recruiting Militants in Southern Thailand, available at http://www.crisisgroup.org/home/index.cfm?id=6170&l=1.


See, for instance, Tom Wright, Hidden Links Bolster Asia Militants," The Wall Street Journal Europe, August 31, 2009.


Recruiting Militants in Southern Thailand, International Crisis Group, June 22, 2009. Available at http://www.crisisgroup.org/home/index.cfm?id=6170&l=1.




"Killings in Southern Thailand on the Rise," New York Times, August 31, 2009.


"Insurgents Turn Up Heat with Hotel Blast," South China Morning Post. March 22, 2008.


"Thailand: Imam's Killing Highlights Army Abuse in South," from Human Rights Watch webpage at http://hrw.org/english/docs/2008/03/26/thaila18346.htm.


"Southern Thailand: The Impact of the Coup," International Crisis Group. March 15, 2007.


Zach Abuza, "Wake Up Call," e-newsletter. March 20, 2007.


"Thai War on Terrorism Presents Diplomatic Headache," Sydney Morning Herald. September 23, 2006.


For more information on Malaysia's 2008 elections, see CRS Report RL33878, U.S.-Malaysia Relations: Implications of the 2008 Elections, by [author name scrubbed].


"Economic Downturn May Push Up Crime, Says Syed Hamid," The Malaysian Insider, June 17, 2008.


The D8 is a group of eight Muslim developing nations comprised of Bangladesh, Egypt, Indonesia, Iran, Malaysia, Nigeria, Pakistan and Turkey.


"Malaysian Premier calls on Muslims to Defy Militants," Agence France Presse, July 20, 2005.


Mohd Nasir Yusoff, "M'sia Wants Stereotyping of Terrorism with Islam to Stop," Bernama, March 5, 2007.


"Muslim Leaders Urge Western Governments to Condemn Acts that Insult Islam," Associated Press, June 9, 2008.


Michael Richardson, "Maintaining Security in Malacca Strait," The Jakarta Post, January 11, 2006.


"Hishammuddin Disputes Claims on Arms Trade," New Straits Times, September 22, 2009.


"Those Linked to Terror Groups to Face Consequences," The Star, December 9, 2007.


For more information, see U.S. Department of State, Country Reports on Terrorism, release on April 30, 2008.


"Move to Abolish Malaysian Security Law Gathers Strength," IANS, June 20, 2008.


Gerakan Mansuhkan ISA, "ISA Itself Has Served as Instrument of Terror of the State," press release, December 3, 2008.


Alan Ting, "Gerakan: ISA Should Be Limited to Anti-Terrorism," Bernama, August 20, 2009.


"ISA, Police Act Amendments to Include Freedom of Assembly," Malaysia Insider, August 20, 2009.


"Deputy Minister Says Tabling of ISA Review Likely Next Month," New Straits Times, September 22, 2009.


U.S. Embassy, Malaysia, Speech by U.S. Ambassador Marie T. Huhta, Rotary International Dinner Forum, Kuala Lumpur, Malaysia, February 22, 2003. http://usembassymalaysia.org.my/amsp0222.html.


For more information on Singapore, see CRS Report RS20490, Singapore: Background and U.S. Relations, by [author name scrubbed].