As part of the war on terrorism, U.S. Defense Secretary Donald Rumsfeld recently called for rebuilding military relations with the Indonesian army. In a joint May 13 press conference with his Indonesian counterpart, Matori Abdul Djalil, Rumsfeld said the Bush administration intended to work with Congress, “to reestablish the kind of military-to-military relations which we believe are appropriate.”

This is hardly a new development. Shortly after Sept. 11, the White House, led by Deputy Secretary of State and former ambassador to Indonesia, Paul Wolfowitz, began maneuvering to loosen restrictions on military aid to Jakarta. The latter had been cut off by the Clinton administration during the Indonesian army’s 1999 rampage in East Timor, which killed thousands of civilians and destroyed 70% of the tiny country’s infrastructure.

But now Bush administration officials argue that the Indonesian army has reformed since the bad old days of two years ago and needs our help in its struggle against terrorism. U.S. intelligence says Osama bin Laden and al Qaeda are active with extremist groups in Java. But if we aren’t careful, the U.S. is likely to find itself in the middle of several very nasty civil wars, which have little to do with jihad, but quite a lot to do with very worldly things like gold, copper, and oil.

There is a good reason why the Clinton administration imposed a ban on military aid to Jakarta. The U.S. has supplied Indonesia with over 90% of its military hardware over the past 30 years. Indonesia has repeatedly put those weapons to deadly use. In 1975 it invaded tiny East Timor, a former Portuguese colony on Indonesia’s eastern edge, now independent. That invasion, according to declassified documents published by the National Security Archives of George Washington University, had the full blessing of then President Gerald Ford and Secretary of State, Henry Kissinger.

According to the United Nations, Indonesia’s 24 years of occupation resulted in the deaths of over 200,000 Timorese, or one third the pre-invasion inhabitants. In terms of percentage of the population, not even Pol Pot managed that kill ratio. When East Timor voted for independence in a 1999 UN-sponsored referendum, the Indonesian army and its militia allies systematically destroyed the country, killing at least 2,000 people and forcing 250,000 more into concentration camps in West Timor.

The Indonesian army is currently engaged in suppressing two other independence movements, one in Sumatra’s Aceh Province and the other in Irian Jaya on the country’s eastern edge. The campaign in Aceh has killed over 6,000 people; 1,500 in the last year alone. In Irian Jaya, which makes up the western side of Papua New Guinea, the Army has been jailing pro-independence supporters and firing on demonstrators. In November, Kopassus, an Indonesian Army unit accused of widespread human rights violations, invited one of Irian Jaya’s independence leaders to a dinner. He ended up strangled to death on the side of the road.

From all indications, that violence is likely to escalate. In a December 29, 2001 speech to military cadets, Indonesian President Magawati Sukanoputri told them: “You can do your duty without being worried about human rights,” a green light to unleash the full fury of the army’s repressive machinery.

While Jakarta says its civil wars are about terrorism, what’s really at stake are billions of dollars in raw materials. The seizure of East Timor allowed Indonesia to claim part of the Timor Gap, a channel between Timor and Australia, estimated to contain anywhere from 1 to 6 billion barrels of oil. While the Indonesians have finally left East Timor, they are hanging onto a section of the Gap. In Irian Jaya, recently renamed West Papua, the army is deeply involved in the logging industry, as well as protecting the investments of the U.S.-operated Freeport-McMoran gold and copper mine and the Atlantic Richfield oil company.

Both Aceh and Irian Jaya’s independence movements were peaceful until army repression sparked a violent response. As Sidney Jones, the Asia Director of Human Rights Watch put it, “the brutality of the army created the mass base for separatist movements.” In the name of fighting terrorism, the Bush administration is about to reestablish ties with a particularly brutal bunch of military thugs. Bad idea the first time around, bad idea the second, and will only inflame rather than douse the separatist fires raging in Indonesia.