“This is part of a deal between the authorities and Abu Bakar,” his lawyer said breezily after one interrogation last week.

That cavalier attitude is only one reason that Indonesia is shaping up as the weakest link in the war on terror in Southeast Asia. The borders of the sprawling archipelago are difficult to police. Corruption is endemic. Officials are leery of offending the country’s 200 million Muslims with a public crackdown. And the Army, once the most efficient institution in the country, has been hobbled by a U.S. ban on the training of Indonesian officers and other military cooperation. “Operational readiness has gone down 60 percent,” says former Defense minister Juwono Sudarsono. Some units have been accused of helping to fund extremist groups like the Laskar Jihad, whose machete-wielding members have fought Christians in the Moluccan Islands.

Fears about Muslim militants’ using Indonesia as a staging ground began mount-ing even before September 11. Last July, five suspected Qaeda operatives slipped into the country, planning to attack the Ameri-can Embassy; Washington was concerned enough to send a secret Delta Force team to Jakarta to beef up security. But the Indonesians apparently allowed the suspects to slip away–and may even have tipped them off, said a U.S. official. Some Indonesian officials continue to waffle over the fact that Al Qaeda ran a terrorist training camp on the island of Sulawesi–despite testimony from alleged Qaeda operatives arrested in Spain–or that they know the whereabouts of Parlindungan Siregar, the man the Spaniards claim ran the camp. “They know where he is,” says a Western diplomat in Jakarta. “They have a tactic of pretending not to know.”

Professionalizing the Indonesian police and military may do the most to pull out Al Qaeda’s roots in Indonesia–and to prevent more from taking hold. The Pentagon has invited Jakarta to submit a wish list of equipment for use in counterterrorist activities, including new choppers. But closer ties are constrained by a U.S. law that bars military-to-military exchanges until Army officers linked to 1999 violence in East Timor are brought to justice. The Indonesians may need to clean up their own house before they can be counted on to clean out any terrorists in their midst.