By Edmund McWilliams

Secretary of State Hillary Clinton's recent visit to Jakarta underscores the importance that the Obama administration appears to attach to Asia and to the U.S. relationship with Indonesia. Indeed, a broad-based, mutually beneficial partnership between the United States and Indonesia can and should be one of the foundations of America's 21st century Asia-Pacific strategy.

But in shaping America's future relationship with that key country, U.S. policymakers should avoid the miscalculations that previously anchored the United States' engagement to Indonesia's anti-democratic, military-dominated elites.

Throughout the Suharto dictatorship and even after his fall, U.S. relations with Indonesia suffered from inadequate attention to creating economic and security ties that improve the lot of the whole of Indonesian society.

For instance, in the past, U.S. economic ties relied too heavily on cheap Indonesian labor, with inadequate attention given to the rights of workers. U.S. investment in Indonesia was also narrowly focused on extractive industries which exploited the archipelago's vast natural resources. While profitable to U.S. investors and their elite Indonesian partners, these investments too often devastated the local environment with ruinous implications.

Forests were destroyed for their timber or to establish oil palm plantations, with no thought to the consequences for the local people for whom those forests constituted homes and a source of livelihood. Massive mining operations poisoned rivers, bays and groundwater. Too often whole communities were displaced in the name of development. Once transferred to another island, their intrusion led to bloody clashes with indigenous populations such as those in West Kalimatan.

The United States has also sought to develop close ties with the Indonesian military through the sale or transfer of weapons, joint training, and senior-level visits. These programs conferred status on senior Indonesian military figures, increasing their chances of promotion. For decades this so-called cooperation was undertaken with no concern for the Indonesian military's problematic record, including ongoing human rights violations, unaccountability before any court, corruption, as well as interference with democracy and insubordination to civilian control.

Too often, U.S. military honors were bestowed on senior officials whose personal records of human rights violations and corruption were widely known within Indonesia. In some instances U.S. support for the Indonesian military rendered the U.S. complicit in war crimes, such as during the invasion and subsequent suppression of East Timor and the less well-known suppression of Papuans.

Beginning in the early 1990s, U.S. cooperation with the Indonesian military was limited, due largely to congressional and public protest as well as the conscientious actions of individuals such as Sen. Patrick Leahy. Most assistance was cut in 1999, during Indonesia's brutal destruction of East Timor following the latter's pro-independence vote, and only gradually restored over the next decade.

Since then, the U.S. government has paid lip-service to human rights concerns by purporting to "vet" individual military personnel slated to receive training. However, the vetting system is ineffective, as shown by a 2005 GAO study.

In response to the threat of terrorism, however, the Bush administration resumed its drive to "partner" with the still-corrupt and unaccountable Indonesian military in 2005. Links between the Indonesian military and terrorist militias, including Islamic fundamentalist ones, did not slow the imperative, which even extended to Indonesia's infamous special forces, the Kopassus.

This effort to build military-to-military relations with an unreformed and unreforming Indonesian military undermined efforts by Indonesians to rein in this rogue institution. The tightening U.S. embrace provided an imprimatur to the Indonesian military that assisted its evasion of real civilian control. Meanwhile, the U.S. has been unwilling to use its resulting leverage to shield those in Indonesia who continue to face intimidation or worse in their efforts to reform the military.

The U.S. is also seeking to expand ties with Indonesia's civilian and military intelligence agencies, BIN and BAIS respectively. Like the Indonesian military, these institutions, led by retired military officials, violate human rights largely with impunity. In 2004, for instance, Indonesia's leading human rights advocate, Said Munir Thalib, was murdered on an international flight. Despite evidence linking the killer to the deputy leader of BIN, that official has not been effectively prosecuted, with several key witnesses inexplicably and suspiciously recanting their testimony.

Cooperation with the Indonesian military and Indonesian intelligence agencies is in the United States' interests. But there is no wisdom in developing partnerships with unreformed institutions. This is particularly the case with regard to the "worst of the worst," the Indonesian special forces.

The U.S. should set specific reform goals against which it will calibrate its cooperation. This was indeed the pledge set forth by Secretary of State Condoleezza Rice back in 2005, when she employed a national security waiver to set aside the final Congressional limitations on aid to the Indonesian military. Needless to say, no plan was put forth and the pledge was not honored by the Bush administration.

Any future military-to-military assistance with Indonesia must be informed by the clear understanding of the Indonesian military's human rights record. As for broader economic and investment ties, they should be formulated to benefit more than just the Indonesian elites, and to encourage the democratization of that very important nation.

Edmund McWilliams is a retired senior U.S. Foreign Service Officer who served as the political counselor at the U.S. Embassy in Jakarta from 1996 to 1999.