Rights campaigners have called on Obama to reverse a recent decision to work with the notorious Kopassus force.
Leaked secret documents show that Kopassus, which was deployed against dissidents under military ruler Suharto, still engage in murder and abduction and target civilians in West Papua, says investigative journalist and author Allan Nairn.
Nairn became well-known when he was imprisoned by the Indonesian military while reporting in East Timor.
“In secret documents from Kopassus, the Indonesian special forces, they state that they have a policy of targeting civilians and targeting churches in Papua,” he told RFI.
“The Kopassus documents specifically include a list of 15 leaders - civic leaders in Papua - and Kopassus defines them as leaders of an independence political movement and as enemies.”
West Papua province is the western half of the island of New Guinea. Separatist movements, sometimes armed, have campaigned against Indonesian rule since annexation in 1969.
The Indonesian military have frequently been accused of brutal repression of the separatists, with alleged video evidence of torture recently causing an internet-fuelled scandal.
The leaked Kopassus list includes “the head of the Baptist Synod in Papua, the evangelical church ministers, intellectuals, students, community leaders,” Nairn says, adding that Obama should cut off assistance to the Indonesian military.
The US recently restored aid to Kopassus, arguing that the force has dropped its Suharto-era habits.
But in his report online Nairn contests that claim.
"When the US restored Kopassus aid last July, the rationale was fighting terrorism,” he writes. “But the documents show that Kopassus in fact systematically targets civilians."
Ahead of Obama’s visit, the East Timor Action Network (Etan) which was set up to support independence for another territory occupied by Indonesia, called for the Kopassus link to be scrapped.
Nairn points out that US companies have major interests in Indonesia, including the world’s largest gold and copper mine in West Papua itself.
“Freeport McMoRan, a US mining company, has a vast mining operation there,” he says. “They run the area like a plantation. In fact for years they have been making payments to the Indonesian military where the Indonesian military essentially work as private security guards.
"They get the money from Freeport and they assault, they abduct, they kill the local people who protest against Freeport.”
For its part, Etan calls on Obama to make US aid conditional on “an end to human rights violations and impunity” and “progress towards full democratisation”.