In a letter sent on the eve of Secretary of State Hillary Clinton's visit to Indonesia, the East Timor and Indonesia Action Network (ETAN) and three dozen other organizations urged her not to offer US assistance to the Indonesian military (TNI) or intelligence agencies.
"The Secretary of State's visit offers the new Obama administration a great opportunity to chart a new course in US relations with Indonesia," said John M. Miller, National Coordinator of ETAN - whose American supporters include Catholic, Jewish, inter-denominational clergy and inter-faith groups.
"We urge Secretary Clinton to promote a forward-looking agenda when she visits Indonesia. Any military assistance should be contingent on human rights accountability and real reform," added Miller. "Secretary Clinton should break with the failed Bush administration policy of engagement with the TNI. The US should once again use military assistance as leverage to promote reform and human rights."
"The TNI looks at US government actions. Statements promoting rights and reforms will be dismissed by the TNI unless U.S. assistance is suspended until genuine progress has been made," according to the letter.
The letter also urges "no resumption of assistance to or cooperation with the notorious Kopassus special forces. They remain the most egregious element of the TNI. There should also be no initiation of assistance to the military and civilian intelligence agencies (BAIS and BIN) which have long records of repressing human rights groups and other critics." BIN is linked to the murder" of Munir Said Thalib, Indonesia's leading human-rights advocate.
"An all-carrot, no-stick approach will undermine efforts to strengthen civilian control of the TNI and achieve judicial accountability for victims of human rights violations," the letter concludes.
ETAN advocates for democracy, justice and human rights for East Timor and Indonesia. ETAN calls for an international tribunal to prosecute crimes against humanity committed in East Timor from 1975 to 1999 and for continued restrictions on US military assistance to Indonesia until there is genuine reform of its security forces. For additional background, see www.etan.org 
The letter in full:
Secretary of State Hillary Clinton
Department of State
February 17, 2009
Dear Secretary Clinton:
As organizations deeply concerned with human rights and justice in Indonesia and East Timor (Timor-Leste), we urge you to make human rights and reform central to your upcoming visit to Indonesia. Like you, we value a strong U.S. relationship with a democratic Indonesia. We recognize that there are a wide-range of issues of mutual concern between the two countries, among them climate change and the global economic crisis.
If you genuinely seek to open a new chapter in U.S. relations with the world's largest Muslim majority nation, we urge you to make clear to Indonesia's leaders that respect for human rights is crucial and that security assistance must be contingent on accountability and real reform. While Indonesia's leaders may balk, its citizens will be grateful.
For far too long the United States government has been an accomplice to human rights violations committed by the Indonesian military. In recent years, U.S. leaders often have paid lip service to human rights accountability and reform. Assistance to the Indonesian military (TNI) expanded rapidly -- despite the lack of any significant TNI reform and despite the ongoing failure to hold the TNI accountable for its past and current human rights violations. Any pretense of conditioning engagement on accountability and human rights evaporated.
Past U.S. administrations have argued that close cooperation with the Indonesian military would spur reform by exposing TNI personnel to democratic perspectives and build respect for human rights and civilian control. However, decades of U.S. collaboration with the Indonesian military has shown no improvement coming from such association. Many U.S.-trained officers were involved in the worst violence in East Timor (Timor-Leste) and elsewhere.
The greatest changes occurred only when the U.S. withheld military assistance, such as foreign military financing and training such as IMET and JCET. For example, during the brief period of serious reform in the years immediately following the resignation of the dictator Suharto, when the separation of the police and military was completed, unelected military officials were removed from Parliament, and East Timor was set on its path to independence.
Now that the U.S. is again engaged with the Indonesian military, international and domestic organizations have documented the Indonesian military's continued resistance to civilian control and oversight.
The TNI continues to evade budget transparency and maintains its widespread impunity for crimes against humanity. The government has yet to release a long-completed inventory of TNI businesses, a crucial step towards the divestment of all military businesses by 2009 as required by law, despite the Defense Minister's repeated pledges to do so. Reportedly, assets have been stripped from many TNI-owned firms. The US State Department's annual human rights report describes TNI prostitution rings in Papua, while illegal logging and extortion of foreign and domestic firms continues there and elsewhere.
UN, State Department and other reports describe Indonesia's human rights courts as incapable of bringing Indonesian military and police perpetrators of serious human rights violations to justice, including those involved in the Tanjung Priok massacre and Abepura (Papua) violence. All those tried by Jakarta's ad hoc Human Rights Court on East Timor were acquitted. No senior officials have been convicted for the widespread crimes against humanity and war crimes committed in East Timor from 1975-1999. Officers credibly accused of serious crimes have continued uninterrupted careers. Several are leading candidates for Indonesia's highest political office this year.
Many in Papua view special autonomy as a failure. The military and police are brutally cracking down on Papuans peacefully-expressing their wish for greater control of their land and protesting environmental degradation and deforestation. In the Maluku and Papua, protesters have received lengthy prison terms for their peaceful dissent.
Retired senior military officials working in Indonesia's State Intelligence Agency (BIN) are suspected of planning and ordering the 2004 assassination of Munir Said Thalib, Indonesia's leading human-rights advocate. They have yet to be successfully prosecuted. The failure to resolve the high profile murder of such a prominent human rights defender puts others on the front lines in defense of fundamental human rights at even graver risk. Human rights defenders in the provinces of Papua and West Papua remain particularly exposed to threats and violence.
The "territorial command system" positions the TNI at the village level and enables their continued involvement in business and politics. This pervasive system poses a threat to upcoming national elections. The TNI-backed fundamentalist Islamic Defenders Front has been intimidating small parties and individuals critical of the military.
The previous administration's pursuit of the TNI as a "partner" in the fight against terrorism raises other fundamental issues. American assistance to and cooperation with the TNI ignores the reality that it is the Indonesian police and not the military that are responsible for tracking down alleged terrorists. (Your department's latest "Country Reports on Terrorism" praises civilian efforts and does not mention the TNI.)
The previous administration pledged to carefully calibrate any security assistance to Indonesia to promote reform and human rights. There is no evidence they ever did so. We urge you to evaluate the impact of U.S. security assistance on accountability, military reform and human rights.
The TNI looks at U.S. government actions. Statements promoting rights and reforms will be dismissed by the TNI unless U.S. assistance is suspended until genuine progress has been made. We urge you to use this leverage and restrict assistance until their substantial progress actually occurs.
We especially urge no resumption of assistance to or cooperation with the notorious Kopassus special forces. They remain the most egregious element of the TNI. There should also be no initiation of assistance to the military and civilian intelligence agencies (BAIS and BIN) which have long records of repressing human rights groups and other critics. As noted above, BIN is linked to the murder of human rights advocate Munir.
An all-carrot, no-stick approach will undermine efforts to strengthen civilian control of the TNI and achieve judicial accountability for victims of human rights violations.