The outrage was global in the late 1990s when Indonesia's military and goon-like militias associated with the army ran roughshod through independence-seeking East Timor. The human rights abuses were so wanton that the United States cut all cooperation with the Indonesian armed forces.
Now just three years later, the Bush administration wants to reestablish assistance to Indonesia's military arguing the world's fourth-largest country and largest majority-Muslim nation is too important to the fight against international terrorism to hold at arm's length.
The idea is sounding alarms among human rights activists and some members of Congress, who fear Indonesia is one more example of how concern for human rights is suddenly taking a distant back seat to national security interests.
"The environment has got much tougher for human rights principles," says Michael Ignatieff, a human rights expert at the Kennedy School of Government at Harvard University. Citing a list of countries to which the US has extended aid or sent military advisers to help fight a terrorist threat including Afghanistan, the Philippines, Georgia, Uzbekistan, and Kazakhstan Mr. Ignatieff adds: "Does the focus on national security really justify ... supplying arms to anyone who waves a flag in our face?"
To these critics, the new era of played-down human rights concerns is alarmingly reminiscent of the cold war. Just as the cold war caused the US to place a premium on friendly regimes over governments that respected democratic rights, the international battle with terror is shrouding human rights concerns.
"During the cold war, anyone who said they were anticommunist got our support, and we often ignored their repressive, corrupt practices, or their involvement in other illegal activity," says Tim Rieser, an aide to Sen. Patrick Leahy (D) of Vermont, one of the US Senate's top human rights watchdogs.
A similar trend is advancing now, he says. Amnesty International places a spotlight on the waning of human rights concerns in its 2002 international report, saying the "gains of many years" have been "set back" by curbs on civil liberties and a resurgence in the power of militaries.
Supporters of military assistance in cases like Indonesia's say that in addition to helping hit terrorism in its cradles, aid also gives the US leverage including in demanding improvements in respect for human rights where it wouldn't otherwise have it.
American leverage with both Pakistan and India in their conflict over Kashmir is as strong as it is because of the military and other ties the US has with both countries, supporters note.
Sounding a similar argument on Indonesia, Deputy Defense Secretary Paul Wolfowitz is aware of the kinds of problems in Indonesia that raise human rights groups' antennae. "The military's problems are significant," he says, noting they have been guilty of "abusing their own people." But Mr. Wolfowitz, a former ambassador to Indonesia, says the risks are too great to leave the sprawling archipelago country without close US involvement helping it along the right path.
"Indonesia's experiment with democracy ... could be a very important model for the rest of the Islamic world," Wolfowitz told a Washington audience last week. "But if it degenerates into conflict ... it could have a severely negative impact on the world."
The US cut off military cooperation in 1999 over abuses during East Timor's fight for independence. Groups monitoring human rights in Indonesia say that not only do military officers involved in past abuses enjoy impunity, but new abuses are also mounting in several provinces.
Wolfowitz, however, says that the government of President Megawati Sukarnoputri is "eager to work with the United States to reform" the military. Working from that premise, the administration earlier this year asked Congress to approve $16 million in antiterrorism assistance to Indonesia: half to create a rapid-reaction force for the remote provinces, half to train the National Police in counterterrorism. The administration also wants to allow military officials eligibility for counterterrorism fellowships.
Congress approved the funding for the national police, but is so far balking at renewing ties to the military. At the same time, two influential senators, Lincoln Chafee (R) of Rhode Island and Russell Feingold (D) of Wisconsin, are calling for both "robust" assistance to the newly independent East Timor and maintaining all restrictions on relations with the Indonesian armed forces.
The Asia director of Human Rights Watch in Washington, Mike Jendrzejczyk, says his work on Indonesia suggests that while the military under President Megawati is "more confident and assertive than ever," there has been little meaningful reform or pressure from the US. One problem, he says, is a "split" in the Bush administration over how much cooperation is warranted, with the State Department less willing than the Pentagon and some White House advisers to overlook human rights abuses.
Others say the issue of assistance to Indonesia will sharpen further as the general debate over human rights and security intensifies. In the case of Uzbekistan, for example, the US continues to be criticized for stepping up military cooperation to a regime that the State Department, in a report released in March, says violently represses political dissidents.
Others question some aspects of the US role in Afghanistan. Harvard Professor Ignatieff pinpoints the dilemma for the US as being how far to cooperate with and encourage some of Afghanistan's local warlords.
"The approach that 'the enemy of my enemy is my friend' is growing, though it's proven to be a poor guide to foreign policy in the past," he says. "It's a recurrent temptation that always gets us in trouble."