An upsurge in violence in disputed corners of Southeast Asia has highlighted the limits to regional antiterror initiatives in the face of unsolved political grievances.
Conflicts once considered to be largely contained are among the recent flare-ups. Security forces in Thailand's mostly Muslim south shot and killed over 100 separatist rebels who launched coordinated attacks last month on police stations across four provinces.
And renewed fighting in Indonesia between Muslims and Christians in Ambon, capital of the Maluku Islands, has left at least 36 dead since April 25.
After being jolted into action by the October 2002 Bali bombings, governments in Southeast Asia tightened the screws on international terrorist groups and their local offshoots. Officials say cooperation has yielded tangible results in the form of more arrests, foiled terror attacks, and tighter financial controls. But joining forces to tackle security threats deemed to be local affairs is less palatable.
Indonesia has insisted on its sovereignty over the Maluku conflict, despite pleas from Christian groups for UN intervention and mediation. The recent riots threaten to undermine a February 2002 peace pact brokered by the government after three years of violence left 5,000 dead. Investigators have since uncovered how Al Qaeda and its affiliates used the years of fighting as a cover for recruitment, indoctrination, and training.
"The government has been successful in uncovering those terrorist networks involved in the Bali bombing," says Dharmawan Ronodipuro of Indonesia's coordinating desk for counterterrorism. "We still have a lot to do to address the long-term root causes [of terrorism]."
In the case of Thailand, the bloodshed made April 28 the worst day of violence since a low-level Muslim insurgency reemerged in January after decades of relative calm. Kuala Lumpur has bristled at Bangkok's allegations that Muslim separatists are taking cover across the border in Malaysia, exploiting close kinship ties between the communities. Malay politicians also criticized Thai troops for storming a historic mosque in Pattani during the fighting.
Over the weekend, Thai Prime Minister Thaksin Shinawatra visited Pattani, where he met with ambassadors and diplomats from at least 12 Muslim countries. He pledged to restore the shot-up mosque, taking a step toward smoothing prickly relations that analysts say confound cooperation against a common threat. "The general feeling is that we can't call on Malaysia for help because this is our business," said Chayachoke Chulasiriwongse, professor of international relations at Chulalongkorn University in Bangkok.
Prime Minister Shinawatra has tried to quash suggestions by his own advisers that foreign terror groups are muscling into the area. However, security forces say that seven of the militants killed April 28 may be Indonesians, raising fears that Jemaah Islamiyah (JI), or another terrorist network, was involved.
For officials trying to clamp down on groups like JI, flare-ups in Thailand and Ambon are a troubling development. The fear is that just as the Maluku conflict has played into the hands of radicals trying to incite terrorism in Indonesia, a festering Islamic insurgency in Thailand could feed a wider cause.
"JI is looking at this area. They have a large pool of wannabe Muslim extremists to draw on," said Paul Quaglia, a security consultant in Bangkok and former CIA official. "They are asking: Is this is a place where we can open up a front for jihad?"
Armed separatists have for decades sought to reclaim three southern provinces that were formerly an independent Muslim sultanate. The rebellion fizzled out in the 1980s, but has since revived with a fresh infusion of Muslim radicals that have stepped up attacks on government targets and personnel.
"You can go after operatives that make bombs and target these individuals, but [southern Thailand] is going back to guerrilla war," says Zachary Abuza, author of Militant Islam in Southeast Asia.
While US officials express concern, they are content for Thailand to handle its own insurgency, saying its government is resolute in tackling radicalism.
A thornier issue is how to approach Indonesia as it sends mixed signals on combating terrorism. President Megawati Sukarnoputri, who is facing a tough reelection bid in July, has depicted the renewed fighting in Ambon as a clash over separatism, rather than interfaith strife. Her advisers say she is wary of angering Muslim politicians, particularly after her party's poor showing in recent elections.
But perhaps the biggest flash point in US-Indonesia relations is the fate of Islamic cleric Abu Bakar Bashir, who was rearrested last month on terrorism charges immediately after serving an 18-month sentence. US officials say Mr. Bashir is linked to Al Qaeda and approved a string of bombings including the Bali attacks.
Muslim leaders have cast suspicion on the arrest, saying it is Washington's handiwork. Hamdan Zulva, a member of a parliamentary commission, said that after the US presented "less-than-believable" evidence as a pretext to invade Iraq, the charges against Bashir could be "trumped up."
• Tom McCawley contributed to this report from Jakarta, Indonesia.