Order Code RL34194
Terrorism in Southeast Asia
September 11, 2007
Bruce Vaughn, Coordinator, Emma Chanlett-Avery,
Mark E. Manyin, and Larry A. Niksch
Specialists in Asian Affairs
Foreign Affairs, Defense, and Trade Division

Terrorism in Southeast Asia
Summary
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 is a base for past,
current, and possibly future 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
anti-American Islamic terrorist groups.
Members of one indigenous network, Jemaah Islamiyah (JI), which has had
extensive ties to Al Qaeda, are known to have 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 12, 2002 bombing in Bali, Indonesia, that killed approximately 200 people,
mostly Westerners. Since the Bali bombing in 2002, which JI is suspected of carrying
out, crackdowns by various governments in the region — encouraged and in some
cases supported by the U.S. government and military — are believed to have severely
weakened the organization, particularly in its ability and willingness to carry out
attacks against Western targets. JI and its cells, however, have not been eradicated
and continue to operate.
To combat the threat, the Bush Administration has pressed countries in the
region to arrest suspected terrorist individuals and organizations 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, increase intelligence sharing
operations, restart military-military relations with Indonesia, and provide or request
from Congress substantial aid for Indonesia and the Philippines.
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 their citizens. 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
will begin with an overview of the rise of Islamist militancy and a discussion of the
JI network before proceeding to discuss terrorism in Indonesia, the Philippines,
Thailand, Malaysia, and Singapore and will conclude with a section on options and
implications for U.S. policy. Counterterrorism strategies include placing greater
emphasis on attacking the institutions that support terrorism, building up regional
governments’ institutional capacities for combating terrorist groups, and reducing the
sense of alienation among Muslim citizens.

Contents
The Rise of Islamist Militancy in Southeast Asia . . . . . . . . . . . . . . . . . . . . . . . . . 1
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
The Rise of Al Qaeda in Southeast Asia . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
The Jemaah Islamiyah Network . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
History of Jemaah Islamiyah . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Jemaah Islamiyah’s Relationship to Al Qaeda . . . . . . . . . . . . . . . . . . . . . . . . 6
Jemaah Islamiyah’s Size and Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Major Plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Indonesia . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
The Bali Bombings and other JI attacks in Indonesia . . . . . . . . . . . . . . . . 12
The Trial and Release of Baasyir . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
U.S. - Indonesia Cooperation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
The Philippines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
The Abu Sayyaf Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
MNLF and MILF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
U.S. Policy Toward the MILF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Thailand . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Southern Insurgency . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
U.S.-Thai Cooperation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Malaysia . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
A Muslim Voice of Moderation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Maritime Concerns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
U.S. - Malaysia Cooperation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Singapore . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
U.S. - Singapore Cooperation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Enhanced Homeland Security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Options and Implications for U.S. Policy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Capacity Building Strategies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Other Policy Implications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Terrorism in Southeast Asia
The Rise of Islamist Militancy in Southeast Asia
Overview
U.S. attention in the region has been focused on radical Islamist groups in
Southeast Asia, particularly the Jemaah Islamiyah 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 has 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
Combating anti-American terrorism in Southeast Asia presents the Bush
Administration and Congress with a delicate foreign policy problem. Most regional
governments also 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 and occupation of 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 The U.S. foreign policy
challenge is to find a way to confront the terrorist elements without turning them into
1 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.
2 Daljit Singh,”The Terrorist Threat in Southeast Asia,” Regional Outlook; 2003-2004.

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heroes or martyrs in the broader Southeast Asian Islamic community. Furthermore,
the 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.
In Indonesia, various schools of Islamic thought have competed for followers
and public attention, but most have not called for an Islamic state. The more radical
groups, which had their roots in anti-Dutch guerilla activities, effectively were kept
in check by strong leadership from Presidents Sukarno (1950-1965) and especially
Suharto (1967-1998). Moderate Islamic groups formed the main legal opposition to
the Suharto regime which ended in May 1998. Since Suharto’s fall, religious
consciousness has been on the rise among Indonesian Muslims, giving greater
political space for radical groups and their violent fringe to operate, at times openly.
The Philippines has had a violent Muslim separatist movement for more than
a century. The Moros of Mindanao and the Sulu Archipelago, including the island
of Jolo, fought a stubborn, bloody, and ultimately futile insurgency against the
American occupation of the southern Philippines following the Spanish American
War (1898). Several Muslim extremist groups in the Philippines have focused their
operations in the relatively isolated Muslim-majority regions in the South.
The southern Thailand provinces of Pattani, Yala, Narathiwat, and part of
Songhkla were once part of an independent sultanate. After Thailand (then called
Siam) incorporated the provinces in 1902, a series of central government-directed
assimilation policies were instituted, which has inspired varying degrees of resistance
from the ethnic Malay Muslim population in the past century that have sought to
preserve their own identity. By the late 1960s, a number of armed separatist groups
had formed, but attempts to forge a broad coalition of resistance failed. In 1981,
Bangkok revamped its approach to the South, emphasizing economic development
and public participation in governance, and encouraging hundreds of fighters to
accept political amnesty. The shift was largely successful and armed movements
weakened, although residual groups became more radicalized and continued guerilla
activities. Through the 1990s, Muslim political participation increased and violence
declined significantly.
In Malaysia, the late 1990s saw a potentially significant electoral swing toward
a radical Islamist party, Parti Islam se-Malaysia (PAS). However, PAS suffered
major setbacks in parliamentary elections in early 2004. The results appear to
indicate that mainstream Islam in Malaysia has reasserted its moderate character.
Prime Minister Abdullah Badawi, who is himself a respected Islamic Scholar, has
demonstrated Malaysia’s moderate Islamic approach since replacing former Prime
Minister Mahathir Mohammad.

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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. The forging of connections between Al Qaeda and domestic radical
Islamic groups in Southeast Asia is part of this trend.
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 has 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
3 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.
4 For examples of how the September 11 plot organizers traveled relatively freely throughout
Southeast Asia to hold meetings and case flights, see The 9/11 Commission Report, pp. 156-

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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
(JI), that 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 network 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.
4 (...continued)
160.
5 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.
6 Zachary Abuza, “Terrorism in Southeast Asia,” in Strategic Asia 2002-2003 (Seattle, WA:
National Bureau of Asian Research, 2003).
7 Zachary Abuza, Militant Islam in Southeast Asia: Crucible of Terror (Boulder: Lynne
Rienner Publishers, 2003).

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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.
JI’s goals have ranged from establishing an Islamic regime in Indonesia, to
establishing an Islamic Khaliphate over Muslim regions of Southeast Asia and
northern Australia, to waging jihad against the West. There appears to be
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 and JI appears to have made Mindanao a primary base
of operations.
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

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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.8
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.9 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.10 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.
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.11 They shared personnel, such as when JI sent an operative with
8 For more information on Indonesia see CRS Report RL32394, Indonesia: Domestic
Politics, Strategic Dynamics, and American Interests,
by Bruce Vaughn.
9 Sidney Jones, “Indonesia Backgrounder: Jihad in Central Sulawesi,” International Crisis
Group Report No74
, February 3, 2004.
10 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.
11 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
(continued...)

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scientific expertise to Afghanistan to try to develop an anthrax program for Al
Qaeda.12 The two networks have jointly planned operations — including the
September 11 attacks — and reportedly have conducted attacks in Southeast Asia
jointly.13 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.14 Riduan Isamuddin, also known as Hambali (for
more information, see below), 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 2002.15
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.16 Its influence transcends these numbers,
however. Many more men have been educated at JI-run pesantrens (religious
boarding schools), where the Baasyir 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 (see Figure 1).
Each mantiqi, in turn, was subdivided into at least three additional layers: battalions,
platoons, and squads.17
11 (...continued)
in Southeast Asia,” p. 9.
12 The 9/11 Commission Report, p. 151. Yazid Sufaat is the individual JI sent to Kandahar.
13 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.
14 The 9/11 Commission Report, p. 151.
15 Sidney Jones, “The Changing Nature of Jemaah Islamiya,” Australian Journal of
International Affairs
, June 2005.
16 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.
17 Jones, “Jemaah Islamiyah in South East Asia,” pp. 27-28.

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However, in practice, JI appears 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. Indonesian expert Sidney Jones has written that
since 2002, a more flexible structure, “better suited for an organization under siege,”
undoubtedly has evolved.18
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. A minority group, led by
Hambali until his capture, is interested in focusing on a broader anti-Western agenda
similar to al Qaeda, and in effecting change in the near term. A leading JI operative
still at large, Noordin Mohammad Top, is believed to lead a splinter cell pursuing
this strategy. 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.19 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.20 The implication
is that JI may not be as monolithic as commonly assumed.21
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.
18 Jones, “The Changing Nature of Jemaah Islamiya,” p. 170.
19 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.
20 Jones, “The Changing Nature of Jemaah Islamiya,” pp. 171-172.
21 International Crisis Group, Jihadism in Indonesia, Asia Report 127, January 24, 2007.

CRS-9
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, apparently 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.22
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.23 (See the Indonesia section below for more
information on the Bali bombings and other attacks in Indonesia.)
Indonesia
In August 2007, Indonesian President Susilo Bambang 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.”24 His statement follows the June 2007 capture
of JI Emir Zarkarsih and JI military leader Abu Dujana, who stated that Bassyir was
the spiritual leader of JI. Earlier in 2007, Indonesian authorities reportedly captured
bomb making materials and ammunition for a grenade launcher in central Java.25
Indonesian authorities also captured 15 JI suspects between March 2007 and the end
22 Romesh Ratnesar, “Confessions of an Al-Qaeda Terrorist,” Time, September 23, 2002.
23 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.
24 “Indonesia’s president Claims Victory in war Against Terror,” DowJones Newswire,
August 16, 2007.
25 Joshua Kurlantzick, “Doing it Indonesia’s Way,” Time Int. Asia, August 20, 2007.

CRS-10
of June 2007.26 In his speech, Yudhoyono stated that the security situation in
Sulawezi and the Malukus had improved. Past inter-communal strife between
Christian and Muslim communities in Poso, Sulawezi, may make that area a focal
point for JI activity aimed at reconstituting their organization.
Others appear less confident over the extent to which JI has been neutralized.
International Crisis Group expert Sidney Jones doubts that any terrorist group in
Indonesia has the capacity to mount a major attack, but is of the opinion that JI has
the ability to recruit new members and to regenerate. “You can’t fully eradicate the
problem. But you can put in place institutions, information-sharing mechanisms and
various controls ... to reduce the scope of threats.”27 In June of 2007, U.S. Pacific
Commander Admiral Timothy Keating stated that JI remained a real threat to the
region.28 Paul O’Sullivan, Director General of the Australian Secret Intelligence
Organization (ASIO) stated in June 2007 that “successful counter-terrorism efforts
by Indonesian authorities have eroded JI’s capabilities but Noordin Mohammad Top
remains at large, and there is no room for complacency.” (See below for more
information on Noordin Top.) He added that “terrorism around the globe is likely to
be a destabilizing force for the next generation.” 29
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
would focus on attacking Western targets, which would include Noordin Top’s
splinter cell, and those who wish to focus their activities on effecting change in
Indonesia. Though recent success by the Indonesian government does appear to have
significantly disrupted JI organization and degraded JI capabilities in Indonesia, JI
does not appear to have been eliminated, and may yet regroup and conduct further
operations in Indonesia in the future.30
Background
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, who was under pressure from Islamic political parties,
condemned anti-American violence and pledged to protect U.S. assets and citizens
26 “Indonesian Authorities Capture 15 Suspects in 3 Months,” Xinhua News Agency, June
22, 2007.
27 “Leaders Shouldn’t Let Terrorism Slip from APEC Agenda-Experts,” DowJones
Newswire,
September 3, 2007.
28 “JI Still Posses a Real Threat, Says US Commander,” The Straits Times, June 29, 2007.
29 Doug Conway, “Warning of Terror to Come,” The Courier Mail, June 21, 2007.
30 “Dujana Admits Bakar was JI Spiritual Leader,” SBS, June 27, 2007.

CRS-11
but also publicly opposed the U.S.-led military campaigns in Afghanistan and Iraq.31
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 Sulawezi and the Malukus offers
terrorists a conflict that they may be able to manipulate to further their ends.32
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.33 The
U.S.-led campaign against terrorism and the war in Iraq have had negative political
resonance in Indonesia. While 95% of Indonesians support religious tolerance, about
3% still support bombings and attacks against non-Muslims.34 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
31 Richard Paddock, “Indonesia Presses U.S. to Stop Bombing Asia,” Los Angeles Times,
November 2, 2001.
32 “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.
33 “Support Declines Among Muslims for Violent Defense of Islam,” Radio Free Europe,
July 26, 2007.
34 Mark Forbes, “JI Openly Recruits as Leaders Quizzed,” The Age, June 23, 2007.

CRS-12
sites frequented by Westerners.35 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.36
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.37 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 Noordin Mohammad Top. Most of the victims
have been Indonesians.
Noordin Muhammad Top, a Malaysian, has been the target of a large manhunt
by Indonesian police for his suspected role of strategist for JI’s major bombings.
Noordin Top’s base of recruits appears to be drawn from like-minded operatives
from JI and increasingly from other militant Islamist groups in Indonesia, such as
those involved in sectarian violence in the Malukus and Poso, and the Philippines.
By 2005, according to some sources, Noordin Top was declaring himself the leader
of Al Qaeda for the Malay Archipelago. Many of the more “mainstream” JI members
reportedly consider Noordin as a danger to the future of the organization.38
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
35 Jay Solomon and James Hookway, “Bali Bomb Suspect Used Thailand as Staging Area,”
The Wall Street Journal, November 7, 2002.
36 R. Pura and L. Lopez, “Bali Blast Signals Militants Rebirth,” The Wall Street Journal,
October 3, 2005.
37 Ellen Nakashima and Alan Sipress, “Al Qaeda Linked to Blast by Official,” Washington
Post
, October 15, 2002.
38 See, for instance, International Crisis Group, Terrorism in Indonesia: Noordin’s
Networks
, Asia Report 114, May 5, 2006; “Profile, Noordin Muhammad Top,” Jane’s
Terrorism & Security Monitor
, November 15, 2006.

CRS-13
Kompak. This is because many of the militants see 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.”39 The increased militant activity in Maluku and Posos 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.40
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 refused to acknowledge his role or
arrest 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 Sukaranoputri
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 2001.41
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.42
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.43 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.44 Only
one witness testified that Baasyir was the leader of JI.45
39 “Weakening Indonesia’s Mujahidin Networks: Lessons from Maluku and Poso,”
International Crisis Group, October 13, 2005.
40 Sidney Jones, “Asking the Right Questions to Fight Terror,” The Jakarta Post, January
9, 2006.
41 Abuza, “Tentacles of Terror,” p. 72.
42 Raymond Bonner, “U.S. Pressure to Hold Militant Sets Off Outcry in Indonesia,” New
York Times
, April 20, 2004.
43 “Bashir: A Strong Chance to walk Free,” Australian Associated Press, February 9, 2005.
44 Sian Powell, “Call for Baasyir Jail Term,” The Australian, February 9, 2005.
45 “Indonesian Prosecutors Ask for Eight-Year Jail Sentence for Bashir,” Voice of America,
(continued...)

CRS-14
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.46 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.47
U.S.-Indonesia Cooperation
Bilateral relations between the United States and Indonesia improved
dramatically in 2005. This 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.48
The Philippines
The Muslim terrorist and insurgency situation in the southern Philippines has
become increasingly complex since 2002 when Philippine and U.S. forces conducted
a relatively successful operation against the Abu Sayyaf Group on Basilan Island off
the southwestern tip of the big southern island of Mindanao. The operation reduced
Abu Sayyaf’s strength from an estimated 1,000 active fighters to an estimated 200-
400 in 2006. Another apparently positive development in the southern Philippines
is that the cease-fire between the Moro Islamic Liberation Front (MILF) and the
Philippine government and military (AFP) has held. Negotiations for a settlement are
also ongoing in Malaysia.
45 (...continued)
February 8, 2005.
46 See, for instance, Michael Sheridan, “Bali Terror Chief’s New Mission,” The Sunday
Times
, August 2006.
47 Mark Forbes, “West Funds Elite Unit to Destroy Islam,” The Sydney Morning Herald,
June 27, 2007.
48 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.

CRS-15
However, there are other developments of a decidedly negative nature that could
worsen the overall situation in the southern Philippines and even the Philippines as
a whole. One is the growing cooperation among the Abu Sayyaf Group, several
major MILF commands, and elements of Jemaah Islamiyah on Mindanao. JI appears
to have made Mindanao a primary base for building up its cadre of terrorists.
Moreover, this cooperation among the three groups appears to be transforming
Mindanao into a significant base of operations rather than just a site for training; and
these operations appear to increasingly target the Philippines for terrorist attacks.
The Abu Sayyaf Group
The Abu Sayyaf Group is a small, violent, faction-ridden Muslim group that
operates in western Mindanao and on the Sulu islands extending from Mindanao. It
has a record of killings and kidnaping and has had past, sporadic links with Al
Qaeda.49 Philippine military operations since 2001, supported by the United States,
have weakened Abu Sayyaf on Basilan Island and in the Sulu islands southwest of
Baslian. However, under the leadership of Khadafi Janjalani,50 Abu Sayyaf
reoriented its strategy and appears to have gained greater effectiveness as a terrorist
organization. Janjalani de-emphasized kidnaping for ransom and instead emphasized
developing capabilities for urban bombings. He improved ties with key military
factions of the MILF and established cooperation with JI. He also re-emphasized the
Islamic nature of Abu Sayyaf. Thus, even though Abu Sayyaf’s armed strength has
fallen from an estimated 1,000 in 2002 to 200-400 in 2006, the capabilities of the
organization may be growing.51 The Abu Sayyaf Group reportedly has established
links with elements of JI, using several MILF base camps where the two groups
reportedly engage in joint training with an emphasis on bomb-making and urban
bombings.52 Two key JI leaders from Indonesia also reportedly relocated to Jolo
Island in the Sulu islands chain.
By mid-2005, JI personnel reportedly had trained about 60 Abu Sayyaf members
in bomb assembling and detonation.53 Since March 2004, the Philippine government
reportedly has uncovered several Abu Sayyaf plots to carry out bombings in Manila,
including the discovery of explosives. In April 2004, police officials reportedly
determined that a February 2004 bombing of a Manila-based ferry, in which 194
49 The ASG reportedly provided support to Ramzi Yousef, an Al Qaeda agent convicted of
planning the 1993 bombing of the World Trade Center. In 1994, Yousef rented an
apartment in Manila where he made plans and explosives in an attempt to blow up 11 U.S.
passenger jets simultaneously over the Pacific Ocean.
50 Khadafi Janjalani reportedly was killed in a shootout with Philippine forces in December
2006.
51 Abuza, Zachary. Balik-Terrorism: The Return of the Abu Sayyaf Group. Carlisle, U.S.
Army War College, 2005. p. 27. Mogato, Manny. "Fighting in the Philippine South Rages,
Soldier Killed." Reuters, November 24, 2005.
52 Ibid., pp. 14-19, 22-24.
53 Mogato, Manny. “Philippine Rebels Linking up with Foreign Jihadists.” Reuters, 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.

CRS-16
people died, was the work of Abu Sayyaf and the Rajah Solaiman Movement (RSM),
a group of Filipino Muslim converts from the Manila area.
Within a few months after the September 11, 2001 terrorist attack on the United
States, the Bush Administration moved to extend direct military support to the
Philippines in combating Abu Sayyaf. The United States committed 1,300 U.S.
military personnel in 2002 to support Philippine military operations against Abu
Sayyaf on Basilan island. This force completed its mission by the end of 2002. In
2005, the Philippines and the United States developed and implemented a combined
operation in western Mindanao against Abu Sayyaf, and U.S. military personnel also
participated in non-combat operations on Jolo Island.
The U.S. military role appears to be based on three objectives: (1) assist the
Philippine military to weaken Abu Sayyaf in its redoubt of Jolo and the other Sulu
islands; (2) neutralize joint Abu Sayyaf-Jemaah Islamiyah training; and (3) kill or
capture Khaddafy Janjalani and other Abu Sayyaf leaders.
MNLF and MILF
The U.S. focus on Abu Sayyaf is complicated by the broader Muslim issue in
the southern Philippines, including the existence of two much larger groups, the
Moro National Liberation Front (MNLF) and the Moro Islamic Liberation Front
(MILF). Both groups have been in insurrection against the Philippine government
for much of the last 30 years. The MNLF signed a peace treaty with Manila in 1996,
which granted limited autonomy to four Mindanao provinces. The MILF, with an
estimated armed strength of 10,000, has emerged as the larger of the two groups. Its
main political objective has been separation and independence for the Muslim region
of the southern Philippines.
MILF leaders deny links with JI and Abu Sayyaf, but there are many reports
linking some local MILF commands with these terrorist organizations. Evidence,
including the testimonies of captured Jemaah Islamiyah leaders, has pointed to strong
links between the MILF and JI, including the continued training of JI terrorists in
MILF camps. 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. A stronger collaborative relationship has developed between these MILF
commands and Abu Sayyaf since 2002.
Zachary Abuza, an expert on Islamist terrorism in Southeast Asia, has identified
four of eight MILF base commands as sites of active MILF cooperation with Abu
Sayyaf and JI. He also has identified the MILF’s Special Operations Group as
facilitating joint training and joint operations with Abu Sayyaf. JI uses these MILF
base camps to train both MILF and Abu Sayyaf cadre. Khadafi Janjalani and other
Abu Sayyaf leaders reportedly received sanctuary in at least one MILF base camp.54
An ambush of Philippine troops on Basilan in July 2007 reportedly was carried out
by a combined MILF-Abu Sayyaf force.
54 Abuza, Balik-Terrorism: The Return of the Abu Sayyaf, pp. 14-19, 22-24.

CRS-17
The MILF has had tenuous cease-fire agreements with Manila. The Republic
of the Philippines government and the MILF concluded a new truce agreement in
June 2003, which has resulted in a substantial reduction in violence and armed
clashes. However, the cease-fire apparently has not reduced the movement of
terrorist personnel and materials between Mindanao and the Indonesian island of
Sulawesi under the direction of JI.55
The negotiations between the MILF and the government have been protracted
and inconclusive. A main issue of disagreement is over “ancestral domain,” the size
and the geographical configuration of an autonomous Muslim political entity.
Another issue is the constitutional-political system in an autonomous Muslim entity;
whether an electoral democracy or a traditional system led by Muslim religious and
tribal leaders. The nature of security forces remains to be resolved, including the
jurisdiction of the Armed Forces of the Philippines and the Philippine National
Police (PNP) in the Muslim entity. The MILF also seeks agreement on a referendum
to be held to determine the final political status of the Muslim entity. Such a
plebiscite could include an option for full independence.
There are divisions between military (AFP) and civilian authorities over strategy
toward the MILF. The AFP favors a more aggressive strategy and is suspicious of
a negotiated settlement. The collaboration between elements of the MILF, JI, and
Abu Sayyaf also suggests that key MILF commanders may not support any agreement
between the MILF leadership and the Philippine government that does not include
outright independence for the Muslim areas of the southern Philippines. In that
scenario, the MILF could fracture with hardline elements joining even more closely
with JI and Abu Sayyaf, which would give rise to a high level of terrorist operations
despite a settlement agreement.
The Arroyo Administration and presumably the Bush Administration are
operating on the assumption that the MILF leadership sincerely wants a peace
compromise and opposes collaboration with JI and Abu Sayyaf. However, there is
another view that the MILF leadership has a relationship with the hard-line MILF
commands similar to that between the political organization Sinn Fein and the armed
wing of the Irish Republican Army. According to this view, the MILF leadership is
acting as a front for the hard-line commands, shielding them from moves against
them by the Philippine government and the AFP.56
U.S. Policy Toward the MILF
The Bush Administration has expressed growing concern over MILF links with
JI and JI’s use of the Mindanao-Sulawesi corridor as well as doubts about the
Philippine government’s ability to end Muslim terrorism on Mindanao.57 The U.S.
55 The Mindanao-Sulawesi corridor is one of the weakest links in the anti-terrorist efforts
of Indonesia and the Philippines backed by the United States.
56 Commentary on ABC Radio News, December 28, 2005.
57 In April 2005, U.S. Embassy Charge d’Affairs in Manila, Joseph Mussomeli, caused an
(continued...)

CRS-18
government has considered placing the MILF on the U.S. list of terrorist
organizations. However, the Arroyo Administration has opposed such a move as
potentially jeopardizing the peace negotiations.58 The Bush Administration also has
voiced support for the Philippine-MILF peace negotiations as the best means of de-
linking the MILF from JI.59 This support boosts the Arroyo Administration’s
position against the AFP’s advocacy of a militarily-aggressive strategy toward the
MILF. Moreover, a breakdown of the negotiations and the cease-fire likely would
confront the Bush Administration with policy decisions regarding a U.S. role in a
wider war. The AFP could be expected to propose increased supplies of U.S. arms
and military equipment; and it likely would argue for a more direct U.S. military role.
The Philippine government might change its previous policy of opposition to a U.S.
military role against the MILF and encourage U.S. actions against the MILF similar
to those in the joint exercises against Abu Sayyaf.
Some analysts have speculated that if significant elements of the MILF opposed
a peace agreement and moved closer to JI and Abu Sayyaf, and if they were able to
continue or expand terrorist operations, the Bush Administration would be faced with
a different kind of challenge, but one that could include similar pressures for greater
U.S. military involvement. There also would be the challenge of maintaining the
U.S. commitment of financial aid to support a settlement. This commitment, too,
could confront the Administration with a policy decision of whether or not to employ
U.S. pressure on the Philippine government to implement faithfully its obligations
under a peace agreement. This scenario is plausible, given the reputed poor
performance of Philippine governments in implementing the 1977 and 1996
agreements with the MNLF.
Thailand
Thailand has endured a persistent separatist insurgency in its majority-Muslim
southern provinces, which includes the provinces of Yala, Narathiwat, Pattani, and
Songhkla, while dealing with political instability in its capital.60 Since January 2004,
sectarian violence between insurgents and security forces in Thailand’s
majority-Muslim provinces has left over 2,300 people dead. In September 2006, an
army commander led a bloodless military coup in Bangkok, ousting the
57 (...continued)
uproar among RP officials when he stated that parts of Muslim Mindanao, with its poverty,
lawlessness, porous borders, and links to regional terrorist groups, could develop into an
“Afghanistan-style” situation. In May 2005, U.S. Ambassador to the Philippines, Francis
Ricciardone, referred to Cotabato province in southern Mindanao as a “doormat” for
Muslim terrorists.
58 Abuza, Balik-Terrorism: The Return of the Abu Sayyaf, p. 42. "Gloria’s powers of
persuasion." Far Eastern Economic Review, December 12, 2002, p. 10.
59 Asia Security Monitor No. 147, November 30, 2005. "U.S. Says Peace Deal in Manila
May Pressure JI." Reuters News, October 22, 2005.
60 For more information on political developments in Thailand, see CRS Report RL32593,
Thailand: Background and U.S. Relations, by Emma Chanlett-Avery.

CRS-19
democratically-elected Prime Minister Thaksin Shinawatra. As the military
government struggled to gain its footing, several coordinated bombs went off in
Bangkok on December 31, 2006, killing 3 and injuring over 30, including 9 foreign
tourists. The terrorist attack in Bangkok has not been linked to southern elements,
but compounds the challenges that Thailand’s new government faces as it tries to
restore legitimacy and democratic rule.
Southern Insurgency
The southern region has a history of separatist violence, 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 death toll
of over 2,300 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.

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 a series of more
gruesome killings, including beheadings, following the Tak Bai incident.

The Thaksin government’s handling of the violence was widely criticized as
ineffective and inflammatory. Critics charge that the Thaksin Administration never
put forth a sustained strategy to define and address the problem, that it repeatedly but
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. Surayud publicly apologized to Muslim leaders
for past government policies in the South and resurrected 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, has advocated negotiations
with the separatist groups as opposed to the more confrontational strategy pursed by
Thaksin.

However, the violence appears to have increased, with the rate of deaths
increasing in the months since the coup. Some analysts say that a younger generation
of more radicalized insurgents is resisting the more conciliatory approach of the new
leadership in Bangkok. As Surayud and Sonthi attempt to win over the trust of the
local Muslim communities, increased attacks make reconciliation difficult to achieve.
Criticism has emerged that Surayud’s announced policies have been insufficiently
implemented, law enforcement has been unable to effectively prosecute cases, and
that intelligence coordination remains abysmal. About 25,000 troops are stationed

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in the South; some say that the military government has shorthanded the South in
favor of redeploying troops to Bangkok and the north to prevent a counter-coup.61
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 incidents to forge
alliances between local separatists and regional Islamic militants. Some of the older
insurgent organizations were linked to JI in the past, have reportedly received
financial support from groups in other Islamic countries, and have leaders trained in
camps in Libya and Afghanistan. Despite these links, however, foreign elements
apparently have not engaged in significant ways in the violence.
Identifying the groups directing the insurgency has been challenging, but most
analysis suggests that there is no one 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 are the
older Islamist separatist groups the Pattani United Liberation Organization (Pulo) and
Gerakan Mujahideen Islam Pattani (GMIP). 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.

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.62 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.63
61 Zach Abuza, “Heading South,” Asian Wall Street Journal op-ed. June 19, 2007.
62 “Southern Thailand: The Impact of the Coup,” International Crisis Group. March 15,
2007.
63 Zach Abuza, “Wake Up Call,” e-newsletter. March 20, 2007.

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Relations with Malaysia are complicated by the ongoing insurgency in the south.
Many of the Muslim Thais are ethnically Malay and speak Yawi, a Malay dialect.
The Malaysian public has grown increasingly angry at the perceived violence against
Muslims in Thailand. Some Thai officials have claimed that there are militant
training camps in Malaysia that feed on the violence in the south. Malaysia denies
the allegations and has pledged cooperation to stem the insurgency. Cooperation
includes increases in troops and equipment to increase border security, joint border
patrols with Thai counterparts, and termination of the joint citizenship privileges that
some believe facilitate the passage of terrorists across the border. After taking office,
Surayud reached out to Malaysia, securing a promise of cooperation from Prime
Minister Abdullah Badawi.
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.64
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 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” have continued, according to the U.S. State Department.
64 “Thai War on Terrorism Presents Diplomatic Headache,” Sydney Morning Herald.
September 23, 2006.

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Malaysia
For a period in the late 1990s, Malaysia was the locus of JI and Al Qaeda
activity in Southeast Asia. In 1999 and 2000, several Al Qaeda operatives involved
in the September 11 and the USS Cole attacks used Kuala Lumpur as a meeting and
staging ground. According to the confessions of one captured Al Qaeda leader,
Malaysia was viewed as an ideal location for transiting and meeting because it
allowed visa-free entry to citizens of most Gulf states, including Saudi Arabia.65
Since 2001, Malaysian authorities have done much in support of the war against
terrorists even as Malaysia has differed with some aspects of U.S. foreign policy.
A Muslim Voice of Moderation
Prime Minister Abdullah Badawi has urged Muslims around the world to guard
against extremism and improve ties with the West while promoting his nation’s
moderate version of Islam known as Islam Hadhari or Civilizational Islam.66
According to Deputy Secretary of State Robert Zoellick the United States remained
confident in Malaysia’s ability to handle the threat of terrorism.67 Malaysia’s former
Prime Minister Mahathir Mohammed, a longstanding promoter of non-violent
Muslim causes, openly criticized Islamic terrorists after September 11, including
Palestinian suicide bombers.
Mainstream Islam in Malaysia appears to have reasserted its moderate character.
The late 1990s saw a significant electoral swing toward the radical Islamist party,
Parti Islam se-Malaysia (PAS), that was reversed in the parliamentary elections of
March 2004 that significantly rolled back PAS’ earlier gains. Badawi’s Barisan
National (BN) party polled 64.4% of the vote and took 196 out of 219 seats in
parliament.68 PAS lost control of Terengganu and only just held on to Kelantan
leaving it in control of only one of 13 state governments, with BN controlling the
rest. PAS seats in parliament fell from 26 seats to seven. The election result was
interpreted as a sign that Malaysians were comfortable with Badawi. The election
result was also viewed as demonstrating the limited appeal of radical Islamic policies
espoused by PAS.69
Maritime Concerns
The threat of seaborne terrorism in the region, particularly in the vital Straits of
Malacca between Malaysia, Singapore, and Indonesia, continues to be a cause for
65 The 9/11 Commission Report, p. 158.
66 “Malaysia PM Abdullah Warns Muslims Against Extremism,” Voice of America, January
27, 2005.
67 “Malaysia’s Efforts Against Terrorism,” Bernama, June 8, 2005.
68 Malaysia Primer, Virtual Information Center, U.S. Department of Defense, April 12,
2004.
69 “Malaysia Politics: Election Winner and Losers,” Economist Intelligence Unit, March 24,
2004.

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concern. This is due to the strategic importance of the sea lanes to international trade
and its vulnerability to attacks against shipping. Malaysia, Singapore, Thailand and
Indonesia 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.70 In August 2007, the navies of Malaysia, Brunei,
the Philippines, Singapore and Thailand participated in a Southeast Asia Cooperation
Against Terrorism (SEACAT) exercise with the U.S. Navy in the Straits of Malacca
that sought to provide training in the area of maritime interception.71
U.S.-Malaysia Cooperation
Malaysia’s Prime Minister Datuk Seri Abdullah Badawi sought to strengthen
bilateral ties with the United States during his July 2004 meeting with President Bush
in Washington, DC.72 Although not uncritical of United States’ policies, such as the
Israel/Palestinian issue, Badawi is a moderate Islamic leader that has demonstrated
that Malaysia will continue to be a valuable partner in the war against terrorism in
Southeast Asia.73 Badawi has urged that the war on terrorism take into account the
root causes of terror and has warned that if it does not “for every one we kill, five
more will emerge to continue their struggle.”74
Badawi’s more diplomatic approach differs from his predecessor former Prime
Minister Mahathir Mohammad. Shortly after taking office in the fall of 2003, Prime
Minister Abdullah Ahmad Badawi pledged to continue Malaysian support for the war
against terror.75 In March 2004, Badawi’s National Front Coalition won a significant
victory over Malaysian Islamists who favor an extreme form of Islam. In a statement
before the Organization of Islamic Conference (OIC) Prime Minister Abdullah
Badawi reportedly called on the United States to change its foreign policy to counter
the perception, held by many in the Islamic world, that it is anti-Islamic.76
In a show of appreciation for his cooperation, Mahathir was invited to
Washington, DC, and met with President Bush in mid-May 2002. During that visit
the United States and Malaysia signed a Memorandum of Understanding (MOU) on
counterterrorism. The text of that document became the basis for a subsequent
70 Michael Richardson, “Maintaining Security in Malacca Strait,” The Jakarta Post, January
11, 2006.
71 “Malaysia, Singapore Boardings Wrap Up Anti-Terrorism Exercise,” US Fed News,
August 21, 2007.
72 See CRS Report RL32129, Malaysia: Political Transition and Implications for U.S.
Policy
, by Bruce Vaughn.
73 Speech by The Honorable Abdullah Badawi, Prime Minister of Malaysia, Washington,
DC, July 19, 2004.
74 “Disquiet as Bush Dominates Agernda at Asia Pacific Sumit,” Agence France Presse,
November 21, 2004.
75 “Malaysia Pledges Terror Fight,” The Wall Street Journal, November 4, 2004.
76 “Time For US to Change its Image,” Today, January 28, 2005.

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declaration on counterterrorism that the United States and ASEAN signed at the
August 2002 ASEAN Regional Forum (ARF) meeting.77 Mahathir’s visit symbolized
positive change in the bilateral relationship. The Bush Administration has
downplayed U.S. human rights concerns over Malaysia’s use of its Internal Security
Act (ISA) to imprison political opponents without trial, especially since Kuala
Lumpur has employed the ISA against suspected members of JI and the Kampulan
Mujiheddin Malaysia (KMM).78
The KMM is a small, militant group calling for the overthrow of the Malaysian
government and the creation of a pan-Islamic state encompassing Malaysia,
Indonesia, 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.
Singapore
Shortly after the September 11, 2001 attacks in the United States, Singaporean
authorities launched aggressive operations to counter terrorist activities.79 Under its
Internal Security Act, Singapore has arrested dozens of suspected Islamic militants,
34 of whom remain in detention. Many of the militants 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 other suspects have links to the Philippines-based Moro Islamic
Liberation Front (MILF).
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. Singapore officials point
to the arrest in Indonesia of Mas Selamat Kastari, the alleged JI Singapore cell leader,
and the arrest in Thailand of Arifin Ali, a senior member of the same cell, as
77 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].
78 U.S. State Department, Patterns of Global Terrorism 2001, pp. 123-124,
[http://www.state.gov/s/ct/rls/pgtrpt/]. The KMM’s links to Malaysia’s main opposition
party, Parti Islam se-Malaysia (PAS), are controversial. After the September 11, 2001
attacks, Prime Minister Mahathir explicitly linked PAS to the KMM and international
terrorist movements, and went on a political offensive against the party, which had made
gains in recent local elections. Several of the alleged KMM members arrested are allegedly
PAS members, including some senior party leaders. Abuza, “Tentacles of Terror,” February
5, 2003 draft, p. 40.
79 For more information on Singapore, see CRS Report RS20490, Singapore: Background
and U.S. Relations
, by Emma Chanlett-Avery.

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evidence of successful intelligence sharing with neighboring countries. 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.
Options and Implications for U.S. Policy
Although Southeast Asian societies and governments in general are more
tolerant, representative, and responsive than those in the Middle East and South Asia,
Islamist terrorist groups have been able to exploit the sense of alienation produced
in part by the corruption and breakdown of institutional authority in Indonesia and
by the marginalization of minority Muslim groups in the southern Philippines and
southern Thailand.
Additionally, to date the U.S. approach to fighting terrorism in Southeast Asia
primarily has been bilateral rather than multilateral in nature. In the near term, barring
another major terrorist attack, it is difficult to foresee these features of U.S. strategy
changing since they are based upon features of international relations in Southeast

CRS-26
Asia: relatively weak multilateral institutions, the poor history of multilateral
cooperation, and the wariness on the part of most regional governments of being
perceived as working too closely with the United States. Addressing these
deficiencies could be elements of the long-term goal of competing against terrorist
ideologies.
Thus far, the strategy of arresting Jemaah Islamiyah’s leadership is thought to
have crippled JI’s capabilities significantly. This may mean that a continued push
to arrest the network’s leadership could dramatically reduce JI’s ability to threaten
Western targets directly. Additionally, it appears that middle and lower-level JI
functionaries’ level of commitment may not be as fanatical as commonly thought.80
However, the apparent ability of JI to remain operational despite the elimination
of most of its leadership indicates that a decapitation strategy alone is insufficient.81
Attacking camps operated by JI and/or the MILF in Mindanao is seen by some as
particularly attractive, as Mindanao may be performing a crucial role as a regrouping
and training area for JI operatives. Such a course of action would need to be
coordinated closely with regional governments to ensure a common front and prevent
antagonizing local governments and populations through unilateral U.S. action.
Capacity Building Strategies
Other counterterrorism strategies include placing a greater emphasis on
attacking the institutions that support terrorism, and building up regional
governments’ institutional capacities for combating terrorist groups and for reducing
the sense of alienation among Muslim citizens.82 Options include:
! Placing priority on discovering and destroying terrorist training
centers, which have proven extremely important to JI and the MILF,
in particular;83
! Strengthening the capacities of local government’s judicial systems,
through training and perhaps funding, in an effort to reduce the
corruption and politicization of the judicial process;
! Working with Indonesia, the Philippines, and other countries to
better manage communal tensions and identify religious flash points
80 Rohan Guanaratna, “Al-Qaeda’s Operational Ties with Allied Groups,” Jane’s
Intelligence Review
, February 1, 2003.
81 Barton Gellman, Washington Post, “Secret Unit Expands Rumsfeld’s Domain,” January
23, 2005. Additionally, in the days after the September 11 attacks, at least one senior
Pentagon official floated the idea of taking military action against terrorist targets in
Southeast Asia as a “surprise” alternative to attacking Afghanistan. The 9/11 Commission
Report
, p. 559, note 75; Douglas Feith, “A War Plan That Cast A Wide Net,” Washington
Post
, August 7, 2004.
82 Abuza, “Funding Terrorism in Southeast Asia,” p. 10-11.
83 Jones, “Indonesia Backgrounder,” p. ii.

CRS-27
before they erupt. Sectarian violence has proven to be fertile ground
for JI and other terrorist groups to recruit and raise funds;84
! Continuing and expanding support for state-run schools, so that
Muslims are less likely to send their children to radical madrassas
where extremist brands of Islam are propagated;
! Expanding educational exchanges, similar to the Fulbright program,
so that future elites have thorough exposure to the United States;
! Strengthening civil society and the democratic process;
! Pursuing policies that encourage economic development;
! Increasing regional cooperation on a multilateral and bilateral basis
with key institutions involved with the war against terror;
! Providing additional assistance and training to developing regional
counter terrorism centers;
! Assisting in developing frameworks such as harmonized extradition
agreements and evidentiary standards to more effectively prosecute
terrorists and facilitate investigations and data sharing with regional
partners;
! Building up the capabilities of countries’ coast guards and navies to
better combat piracy, gun running, and other types of smuggling,
particularly in the Straits of Malacca and the waters between
Sulawesi and the southern Philippines;
! Continue to track terrorism financing. Notwithstanding increased
police cooperation, most Southeast Asian countries do not appear to
have made commensurate efforts to locate, freeze, and at a minimum
disrupt the flow of the assets of Islamic terrorist groups.
! Increase U.S. Pacific Command’s use of international conferences
and exercises aimed at combating terrorism and piracy.85
Other Policy Implications
There appears to be a perception among some Southeast Asians that the United
States has relied too heavily on “hard” power to combat terrorism, not only in
Afghanistan and Iraq, but also in Southeast Asia. Malaysian Defense Minister Najib
Razak, for instance, has stated that “terrorism cannot be bombed into submission ...
the underlying legitimate grievances that allow for such extremists to gain support”
must be addressed. He advocates “a judicious mix of hard and soft force” to prevail
against terrorism. Some regional academics also have concluded that America’s
“highly militarized approach” to the war against terror in Southeast Asia may be
inadequate to neutralize the threat and may “even backfire.” “The embers of radical
Islamist terrorism can only be doused by the adoption of a comprehensive approach
84 Sidney Jones, “Terrorism In Southeast Asia, More Than Just JI,” Asian Wall Street
Journal
, July 29, 2004.
85 United States Pacific Command Joint Interagency Coordination Group for Combating
Terrorism, “Strategy for Regional Maritime Security Initiative,” Version 1.0, November,
2004.

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that addresses a host of real or perceived social, economic, political, and ultimately
ideological challenges.”86
Some analysts believe Southeast Asian states perceive the United States as
focused on the war against militant Islamists to the exclusion, or significant
undervaluation, of other issues of more concern to regional states. Added to this are
regional perceptions of an overly militaristic U.S. response in Southeast Asia. There
are others still that see the American war on terror as a war against Islam. Together
these factors indicate a potential disconnect between the United States and regional
states. Such a division has the potential to limit the degree to which regional states
will cooperate with the United States. From one perspective, “Washington stands to
lose ground against Beijing’s diplomatic drive to court regional countries on other,
equally important economic and strategic issues if it remains narrowly focused on
counter-terrorism cooperation alone.”87 A policy approach that focuses more attention
on the region and does more to take into account the concerns of regional states
could, in this view, potentially achieve more cooperation in areas of concern to the
United States including counterterrorism cooperation.
86 See Seng Tan and Kumar Ramakrishna, “Interstate and Intrastate Dynamics in Southeast
Asia’s War on Terror,” SAIS Review, Spring, 2004.
87 Amitav Acharya and Arabinida Acharya, “The Myth of the Second Front: Localizing the
‘War on Terror’ in Southeast Asia,” The Washington Quarterly, Autumn, 2007.


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Figure 1. Southeast Asia


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Figure 2. Indonesia


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Figure 3. Malaysia and Singapore


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Figure 4. The Philippines


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Figure 5. Thailand