General Wiranto and the 1999 Deal to Ignore Militia Massacres
By Desmond Okafor ·
The Clinton administration chose to ignore "overwhelming" evidence of military-led atrocities in East Timor to secure a security pact with General Wiranto.
The people of East Timor, a Southeast Asian territory fighting for independence from Indonesia, paid for American diplomacy in blood and ash. In the summer of 1999, as they prepared to vote for their own freedom, they were hunted by pro-Indonesia militias that burned villages and slaughtered civilians while the soldiers meant to protect them looked on or held the triggers.
We have the record of the deal that allowed this to happen. What survives in the archive is a curated description of the talking points used by Stanley Roth—the Assistant Secretary of State for East Asian and Pacific Affairs from 1997 to 2001—during a mission to the region in July 1999. The record establishes that Roth met with Indonesian President Habibie, the scientist-engineer who had succeeded the longtime dictator Suharto in 1998, and Xanana Gusmao, the resistance leader who would eventually become the first president of a liberated Timor-Leste. But the pivotal exchange was with General Wiranto, the Commander of the Indonesian Armed Forces from 1998 to 1999 and a man who would later serve as the chairman of the Presidential Advisory Council.
Not now question of blame
On July 12, 1999, Roth sat down with Wiranto. The record shows that Roth entered that room fully aware that the Indonesian National Armed Forces—the TNI, the military apparatus that had spent decades suppressing Timorese independence—were not neutral observers. The record explicitly notes that Roth acknowledged "overwhelming multi-source evidence of continuing close cooperation with militias by elements of TNI" in East Timor.
In any sane ethical framework, "overwhelming multi-source evidence" of state-sponsored mass murder is a stop sign. It is the moment where diplomacy ends and sanctions begin. Instead, the record shows the Clinton administration treated this evidence as a footnote. Rather than demanding an accounting for the blood already spilled, Roth’s talking points conclude that the administration "trusts Wiranto is committed to military neutrality in East Timor."
The record contains the most damning sentence of the mission: Roth determined there was "not now question of blame but results."
By erasing "blame" from the conversation, the U.S. didn't just overlook a few rogue soldiers; they signaled to the Indonesian military that the carnage was an acceptable cost of doing business. The desk's reading is that this "trust" in Wiranto functioned as a mechanism for strategic ignorance. By tethering U.S. policy to the personal word of one general, the Clinton administration created a diplomatic loophole that allowed them to maintain a security relationship with the TNI while formally acknowledging the atrocities the TNI was committing.
Document imagery from nsarchive.gwu.edu From the files: nsarchive.gwu.edu
The lever of normalization
Why would the U.S. ignore the screams of the Timorese? The record provides the currency of the trade. Roth’s talking points make it clear that the primary objective was not the prevention of a massacre, but the restoration of the U.S.-TNI security architecture. The record states that the "TNI contribution to Indonesia's democratization key to establishing more normal military-military ties with U.S."
This was the lever. The U.S. wanted its military ties back. It wanted a stable, pro-Western military partner in Southeast Asia to anchor regional security. The fate of East Timor was not the goal; it was the bargaining chip. The public record shows that the U.S. had conditioned the normalization of these ties on the TNI's commitment to democratization, but the talking points reveal how thin that condition actually was.
There is a profound irony in the way Roth used "democratization" as a buzzword while ignoring the systematic dismantling of democratic safety in East Timor. The pattern suggests that the primary U.S. objective was the restoration of the security architecture, rendering the actual survival of the Timorese people a secondary diplomatic concern. The U.S. was not trying to save East Timor; it was trying to save its relationship with the people who were destroying it.
A performance of leverage
If the U.S. government truly believed that "normal military-military ties" were the only way to force the TNI toward neutrality, it would have built a framework of consequences. But the record shows no such thing. There are no mentioned sanctions for failure. There is no timeline for the withdrawal of aid if the militias continued their raids. There is only "trust."
If this file is shaped the way it looks, the talking points represent a performance of leverage rather than a credible threat. Roth was playing the part of the stern diplomat, but he was offering a reward for a promise he knew was likely a lie. By prioritizing "results" over "blame," the U.S. effectively told Wiranto that as long as the optics remained manageable, the ground-level violence would not jeopardize the eventual return of U.S. military cooperation.
This created a perverse incentive for the TNI. The diplomatic mission provided a green light of plausible deniability. It signaled to the Indonesian military leadership that personal assurances from the top—the "trust" of a man like Wiranto—would outweigh the "multi-source evidence" of violence on the ground. The TNI didn't have to stop the militias; they just had to make sure the U.S. felt comfortable pretending they had.
The cost of the green light
The timing of this visit is the final, most cutting piece of the puzzle. Roth’s meeting took place on July 12. The referendum for East Timorese independence was scheduled for August. The gap between these two dates was not a window for peace, but a window for preparation.
The pattern suggests that the U.S. was attempting to manage the optics of the upcoming referendum rather than prevent the subsequent violence. By granting Wiranto this blanket of trust just weeks before the vote, the U.S. ensured that the Indonesian military felt secure in its standing with Washington, even as it prepared the militias for the scorched-earth campaign that followed the independence vote.
The desk's reading is that the still-withheld pages of this era's correspondence would show a calculated decision to trade Timorese lives for Indonesian military cooperation. The "overwhelming evidence" was not a failure of intelligence; it was a known factor that was consciously discarded to protect a security partnership.
General Wiranto would go on to remain a powerhouse in Indonesian politics for decades, eventually serving as a Coordinating Minister for Political, Legal, and Security Affairs. He was never held accountable by the U.S. for the blood on his hands in 1999. The price of that "trust" was paid by the thousands of Timorese who were murdered, displaced, or disappeared in the weeks after August. The record shows us exactly who decided that their lives were worth less than "normal military-military ties."