Published in The Earth Times Magazine (March 2002)

There is no issue more pivotal to the future of the terror war in Southeast Asia than the relationship between the U.S. and Indonesia’s generals. Nor is there any relationship fraught with more pitfalls.

Under the armed forces’ policy of dwifungsi, the military is responsible for safeguarding the state against both external and internal security threats. That makes the generals the gatekeepers of the terror war. Unfortunately for American policymakers, they come with a whole warehouse full of baggage — much of which the U.S. helped them pack.

From one end of that vast country to another, the Indonesian armed forces, known by the Indonesian initials TNI, have carved a path that has left even their defenders crying for reform.

“Members of both the TNI and the police committed numerous serious human rights abuses,” the State Department’s own 2001 Human Rights report stated.

Yet the geo-political realities of Indonesia’s strategic position on one of the world’s most vital sea lanes, its wealth of natural resources, and its role as the fourth most populous nation on earth, mean the U.S. has a long history of tempering outrage with pragmatism.

Throw in the fact that Indonesia is the world’s largest Moslem country with potential to become the rear-base of Islamic terror, and realpolitics are likely to once more overshadow talk of Indonesian human rights in the White House.

Like Suharto himself, the military has been a handy tool for U.S. foreign policy since the mid-60s. After Suharto crushed Southeast Asia’s large communist party in a 1965 coup that left as many as 500,000 dead, then-Defense Secretary Robert McNamara told President Johnson that American military aid “encouraged [the army] to move against the communist party when the opportunity was presented.”

Ten years later, President Gerald Ford and Henry Kissinger gave Suharto the green light to invade the former Portugese colony of East Timor when they visited Indonesia just days before the assault was launched. The 24-year occupation ultimately claimed as many as 200,000 lives.

Since then, the U.S. has provided Indonesia with about $1 billion in military aid and training. But that has been an on-again, off-again affair as congressional critics have reacted to various accusations of military atrocities.

The most vivid example came in the weeks leading up to the UN-mandated independence referendum in East Timor in 1999. Half the population was driven from their homes and as many as 1,000 were killed in a paroxysm of violence carried out by pro-Indonesia militias bought and paid for by TNI.

At the time, few knowledgeable observers doubted that the scorched earth policy was the military’s way of sending a message to other restive provinces. One Indonesian commander in East Timor said as much in an interview before the vote: “I would like to convey the following: If the pro-independents do win,” warned Col. Tono Suratman, “all will be destroyed.”

The Australian media would later reveal that Australian intelligence had evidence “top-level military officials and cabinet secretaries” had orchestrated the terror. The UN Commission of Inquiry on East Timor concluded that the “intimidation and terror attacks … would not have been possible without the active involvement of the Indonesian army, and the knowledge and approval of the top military command.”

Yet when a Jakarta court convened in late March, it was three mid-ranking Indonesian army officers who went on trial for taking part in the massacres. The generals were in the gallery lending their moral support — and sending a clear message that the military is not afraid of civilian authorities.

The trial was the result of pressures for military accountability coming from some sectors of Indonesia’s nascent democracy, but the fact that the top commanders were still walking free demonstrated that the military remains the most powerful institution in the country today.

Such contradictions will continue to complicate the American terror war as the Administration wrestles with Congress over whether Indonesia is satisfying the requirements of the so-called Leahy Amendment to the Foreign Operations Appropriations Act. Passed by Congress in the fall of 1999, the measure bans a resumption of U.S. military ties with Indonesia until members of the military involved in human rights violations in East Timor are brought to justice.

For the Bush White House, that law is now a severe inconvenience.

Advocates of continued U.S. military relations with Indonesia have long argued that a severing of direct contacts is an obstacle to reform. Among them are some of the men now calling the shots in the terror war.

“We have in the past worked with the Indonesian armed forces and are eager to continue to do that in the future,” then-Secretary of Defense Dick Cheney said in Jakarta a few months after Indonesian soldiers opened fire on a funeral procession in East Timor, killing 271 people.

Washington’s advocates of military ties point to the pivotal role played by then-armed forces commander, Gen. Wiranto, in convincing Suharto to resign in 1998, thus heading off a potentially bloody revolution, as evidence of the strength of their argument that the Indonesian officer corps can be influenced to respect democratic ideals.

The critics just as readily point to the fact that the military’s point man in the war on terror, Lt. Gen. Kiki Syahnakri, was martial law commander in East Timor during the scorched-earth campaign.

When President Megawati Sukarnoputri visited Washington in the days after Sept. 11, President Bush promised more than $700 million in economic aid, including police training and civilian courses in defense. He also expressed a desire to resume some level of direct military contacts and “non-lethal” weapons sales.

The comments set off a firestorm among Indonesia’s critics.

“As President George W. Bush builds an international coalition to fight terrorism, he is in danger of arming and training some of the Pacific region’s worst tools of terror — namely the Indonesian military,” wrote Frida Berrigan of the World Policy Institute.

Those concerns have since been repeatedly echoed on Capitol Hill.

“Some of their top military officers, including some still serving, planned, orchestrated and then covered up the attacks in East Timor,” Sen. Leahy charged in March. “As long as they are running things, with nothing done to hold them accountable, it would be premature for us to launch joint operations.”

In part because of such domestic political realities — but also because no one in Indonesia seems to want them — Deputy Defense Secretary Paul Wolfowitz, a former U.S. ambassador to Indonesia, recently announced that the administration had concluded it would be “counterproductive” to deploy U.S. troops in Indonesia. Still, the administration is likely to continue arguing that national security outweighs human rights concerns in the age of terror.

“The trick is to find ways to move forward that encourage reform in the Indonesian military,” Wolfowitz told The New York Times, “rather than turn a blind eye to some of the past problems.”

But some days, reform seems a matter of one step forward, two steps back.

In the latest example, the military announced that it’s own investigators would charge several officers in the murder of Papuan independence leader Theys Hiyo Eluay. On the surface, it was good news for the reformers.

Among the military’s critics, however, that optimism was tempered by the knowledge that the officer who made the announcement, Maj. Gen. Syafrie Samsuddin, was in 1998 commander of military units blamed for killing protesting students at Jakarta’s Triskati University, an incident that sparked bloody riots that left 1,500 dead. Even worse, the critics also knew that Syafrie, who had steadfastly refused to respond to a Commission on Human Rights investigation into the shootings, had just been promoted to the job of chief spokesman for the armed forces.

An officer accused of overseeing the murder of the nation’s children on the streets of the capital was now the Indonesian military’s most public face.

By Lawrence Pintak

Lawrence Pintak is an award-winning journalist and scholar. He is a former CBS News Middle East correspondent and was founding dean of the Edward R. Murrow College of Communication at Washington State University (2009-2016). He was named a Fellow of the Society by the Society of Professional Journalists in 2017 for "outstanding service to the profession of journalism" around the world. Pintak is a contributor to, The Daily Beast, and other outlets. Read his articles at His books include Reflections in a Bloodshot Lens: America, Islam & The War of Ideas; Islam for Journalists (co-editor); The New Arab Journalist; and Seeds of Hate: How America’s Flawed Middle East Policy Ignited the Jihad. He holds a PhD in Islamic Studies from the University of Wales, Trinity St. David. Follow him on Twitter @LPintak.

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