Indonesia's military, and in particular its Kopassus special forces, have an abysmal rights record in past campaigns against separatists in East Timor, West Papua and Aceh.
The United States and Indonesia have plenty of common security interests, but US President Barack Obama faces a difficult stumbling block when discussing closer military ties during his visit this week -- human rights.
Indonesia's military, and in particular its Kopassus special forces, have an abysmal rights record in past campaigns against separatists in East Timor, West Papua and Aceh. A new video showing the torture of Papuan men has brought the issue back under the spotlight as Obama visits Indonesia.
The two countries have a longstanding security relationship. Indonesia's Detachment 88 anti-terrorist unit, set up after the 2002 Bali bombings, is funded, equipped and trained by the United States and Australia, and has scored impressive successes.
The militant threat in Indonesia has been greatly reduced in the past decade. Groups loyal to al-Qaeda have been scattered and many key leaders have been killed by forces from Detachment 88. Obama needs to ensure that close cooperation continues in the fight against militancy in the world''s biggest Muslim country.
Jakarta, too, wants to foster security ties, partly to act as a bulwark against an increasingly hawkish China which has been flexing its muscles in territorial disputes in the South China Sea with some of Indonesia's southeast Asian neighbours.
"I think any president in the US must take Indonesia as a good friend," said Indonesian security analyst Noor Huda Ismail, vice-president of Sekurindo Global Consulting.
"They have no choice but to make friends with us because we will be their bastion in the region, to contain China." Obama's balancing act is to foster and deepen security cooperation without appearing to condone human rights violations by Indonesia's military and police.
His Indonesian counterpart Susilo Bambang Yudhoyono also has a balancing act to perform. China is the dominant power in Asia, in economic as well as military terms. In his cooperation with Washington, Yudhoyono must try to avoid antagonising Beijing.
In July, Defense Secretary Robert Gates announced during a visit that Washington was ending its ban on ties with Kopassus. He said this followed steps by Indonesia to remove convicted human rights violators from the ranks of the special forces.
But human rights organisations reacted with outrage, saying Kopassus still harbours officers guilty of crimes against humanity. And the leaking of a video showing the torture of Papuans, where a low-level separatist insurgency has simmered for decades, has made the issue even more sensitive.
The video shows two Papuan men being interrogated and tortured. They are beaten and kicked. One man has a knife held to his throat, and another has a burning stick held to his genitals.
Data on the video -- which appears to have been filmed with the mobile phone of one of the interrogators -- suggests it was taken on May 30 this year. It is not clear what unit of the Indonesian security forces was involved.
"The US seems to be very cautious on military cooperation with Indonesia, and one of the main problems is Papua," said Andi Widjajanto, security analyst at the University of Indonesia.
"It is more of a problem now with the release of the video tape of Indonesian military torture."
What makes the issue even more sensitive is many Indonesians accuse the United States of double standards -- particularly after numerous reports of American abuses in Iraq and Afghanistan, above all the Abu Ghraib scandal.
Some Islamic groups in Indonesia say the United States is waging a war against Islam and only cares about the human rights of Christians. Papuan separatists are Christian, as were the East Timorese who won independence from Indonesia in 1999 after decades of heavy-handed military efforts to crush them.
Detachment 88, too, has been accused of rights abuses.
Ismail said that if the battle against militancy in Indonesia was to be won, it was essential that security forces were able to capture hearts and minds and avoid alienating Muslims.
"Most of the assistance from the US for Detachment 88 is by providing weaponry, but if you look at the situation, it is a narrative war, you cannot really counter narrative with bullets, you have to counter with another narrative," he said.
Also, Kopassus remains a highly influential political force. Many of Indonesia's leading politicians are former officers in the special forces. Yudhoyono's brother-in-law is a former head of Kopassus and is tipped as a future Indonesian army chief.
"Kopassus is a machine for making Indonesia's future leaders. Strategic army posts in this country are almost always filled by Kopassus officials," Widjajanto said.
"With the US not co-operating with Kopassus it is losing its chance to get closer ties with future Indonesian political and military leaders."
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