An Australian report has accused the Indonesian military of committing widespread human rights abuses in the restive eastern province of Papua.
Clashes between locals and security forces are frequent in Papua
The report, by the Centre for Peace and Conflict Studies at Sydney University, gives accounts of rape and torture.
It also accuses the military of training local government militias.
The report's publication comes just two days after Indonesian President Susilo Bambang Yudhoyono called for a peaceful solution to Papua's separatist unrest.
Papua, formerly known as Irian Jaya, has been a scene of secessionist violence since Dutch colonial rule formally ended in 1962.
The head of the Centre for Peace and Conflict Studies, Stuart Rees, said Australia was a signatory to the international convention on genocide.
"That gives us a legal obligation as well as a moral obligation to tell a wider public what is going on."
The report says there has been a recent increase in large scale military campaigns in Papua, which are "decimating highland tribal communities".
"Military operations have led to thousands of deaths in Papua and continue to costs lives, yet [Indonesia's] armed forces act as a law unto themselves with no real accountability for crimes against the Papuan population," the study alleges.
It also claims the government is involved in recruiting and training pro-Jakarta militias in the province.
The report's authors say that if their concerns are not acted upon, there may be a serious threat to the survival of the indigenous people in the province.
But a spokesman for the Indonesian army has rejected the allegations of rape and civilian killings.
"Indonesia's armed forces do not have an interest in doing such things. Our duty is to protect people in Papua from the separatists," Colonel Ahmad Yani Basuki told the BBC's Indonesian service.
"There is a possibility of one or two troops who violate the rules, but it doesn't necessarily mean all of them are doing it.
"We will take action on those who conduct violence against civilians."
Mr Yudhoyono spoke about the continuing violence in Papua during his annual speech to parliament on Tuesday.
He ruled out independence for the province, but said a solution involving a form of special autonomy needed to be sought.
"The government wishes to solve the issue in Papua in a peaceful, just and dignified manner, by emphasising dialogue and a persuasive approach," Mr Yudhoyono said.
He also spoke about another area of unrest, the province of Aceh.
Rebels from the Free Aceh Movement (Gam) have recently signed a peace deal with the government. Mr Yudhoyono promised to honour the agreement and make sure it was implemented on the ground.