The recent deaths of two independence leaders, plus increasing harassment against activists and civil leaders, suggest that the Indonesian government is using the US-led counterterrorism campaign to justify its ongoing efforts to stamp out separatists.
In Aceh, Abdullah Syafii, commander of the Free Aceh Movement (GAM), died Tuesday in a gun battle with Indonesian troops, who tracked him down at his jungle camp. Analysts say the killing is a serious blow to GAM, which has been fighting for 25 years to win independence.
The latest military push comes as US and other foreign governments are leaning on Indonesia to find militants accused of plotting with terror groups linked to Al Qaeda.
Despite a string of recent arrests in Singapore and Malaysia that point to the involvement of radical groups in Indonesia, the government has tended to tread softly for fear of provoking its majority Muslim population.
"From a military point of view, [Syafii's death] is a significant success," says Saad, who now heads a human rights foundation. "But will it contribute to a permanent solution to the problems of Aceh? I don't think so."
Analysts say the military has sought to paint Aceh, which has a conservative Muslim tradition and whose rebels are often portrayed as militant Islamists, as an antiterror crusade.
"It's in Indonesia's interests to say that any Muslim militants are essentially the same as Al Qaeda," says Harold Crouch, local director of the International Crisis Group, a think tank.
In West Papua, police are investigating the November abduction and murder of Theys Eluay, a pro-independence politician. The local police chief says that rogue troops may have been involved in the abduction, which occurred on a road dotted with military checkpoints. The government is assembling an independent inquiry team.
Activists claim Eluay was murdered by special-forces soldiers known as Kopassus which, under ex-President Suharto, were accused of operating death squads in trouble spots in Indonesia.
Although Syafii and his fighters lived by the sword, the clamp-down on separatists hasn't only been in the theater of war. Police have used antisubversion laws to jail activists who advocate independence for Aceh, and are currently pursuing a similar case against three members of an Irian Jaya group that was originally sponsored by ex-President Abdurrahman Wahid.
The Indonesian Army has increased troop numbers in Aceh over the past year and wants to install a special military command in the province, a move opposed by human rights activists.
"The space for human rights and democracy is getting narrower in Indonesia," says Hasballah Saad, an Achenese who served as minister of human rights under former President Wahid. Since President Megawati replaced Mr. Wahid in July, she has stepped up the rhetoric against separatists, telling troops to worry less about human rights abuses and get the job done.
Aceh and West Papua have benefited from new autonomy laws promising a greater share of revenues. Aceh's independence calls largely stem from human rights abuses by the military, and resentment over the sliver of its wealth that Jakarta gave it after exploiting its natural resources.