DAVID MARK: An elite counter-terrorist police unit in Indonesia has been accused of carrying out a mass killing in a village in the central highlands of West Papua. The unit was partially trained and supplied by Australia Federal Police.

Activists says 11 people are dead and 20 more are missing after a combined military and police crackdown on support for the Free Papua separatist movement. The names of victims and several grisly photographs have been provided to PM by the armed wing of the movement.

It's impossible to verify the claims, but Indonesia's Embassy in Canberra has agreed to take up the matter.

Peter Lloyd reports.

PETER LLOYD: It's the least populated but most restive corner of our vast near neighbour. For 50 years Papuans have agitated for independence from their Javanese masters. It's a campaign that's been bitterly fought on both sides.

In recent weeks the pace of violence has quickened, especially in the Central Highlands. Shootings have become so frequent that locals have taken to calling it the Gaza strip.

It's from this territory that these shocking claims of extra judicial killings are emerging.

The spokesman for the military wing of the Free Papua Organisation is Jonah Wenda. We conducted an interview via an exchange of text messages after telephone communications failed. He told me that an entire village had been targeted.

JONAH WENDA (voiceover): Indonesian government fear this village is a strong hold of freedom fighters in the Centre Highlands of West Papua. TNI and police did this. They were picked from different places like school, gardens, on the road and even taken from their home and kill them and throw them in the bush, side of the road and threw in the river.

PETER LLOYD: Jonah Wenda emailed the names of 11 people he says were killed in the crackdown, all civilians. He also provided several photographs of corpses that appeared to have been beaten and suffered serious injuries. He also says there are two instances of rape.

None of these claims can be verified, though they are strikingly similar in nature to allegations of human rights abuses by the Indonesian security forces. One of the most notorious units, known as Densus 88, is partially equipped and trained by the Federal Police.

Shortly after our exchange, Jonah Wenda sent a message to say that he had been arrested by police. He says he is being held at a police station in the provincial capital.

In the past, activists have been beaten, tortured and killed after being taken away by the authorities.

Academic Professor Damien Kingsbury from Deakin University has been studying the decades-long struggle by the Indonesian state to exert its will over West Papua. He believes the claims of a mass killing are consistent with an upswing of violence and intimidation across the province.

DAMIEN KINGSBURY: The information we've received today from West Papua is consistent with information we've been receiving over the past couple of weeks. This is more detailed, it's more comprehensive but it's absolutely in line with the other information we've received and it comes from a reliable source so we believe it to be accurate.

PETER LLOYD: Why is this kind of violence breaking out and why does it appear to be getting worse?

DAMIEN KINGSBURY: Well there's always been a background of violence in West Papua and the Indonesian military and the police in particular, the anti-terror group there, have always taken a very strong line against what they perceive to be separatists sentiments by West Papuans.

But the West Papuans themselves are really looking for a negotiated settlement to the problems of the province and they're pushing that agenda by engaging in things like flag-raising ceremonies to demonstrate their unhappiness. That's perceived to be a sign of separatist intent and the army and the police are cracking down on it.

PETER LLOYD: The claim here seems to be that one particular village was targeted because the TNI allegedly believed that the residents of that village were separatists, if not taking up arms at least supporting, encouraging and giving safe haven to them?

DAMIEN KINGSBURY: Well that may be the case or that may be what they believe but of course if anybody is engaged in unlawful activities of course they should be arrested and charged and taken through a due process rather than summarily executed.

And I think this is the nub of the problem in West Papua; that the military and the anti-terror police take it into their own hands to engage in trial and execution on the spot without going through due process. And it's not based on evidence, it's based on supposition, on rumour, on belief and there's huge problems with this and it only builds further resentment.

DAVID MARK: Professor Damien Kingsbury from Deakin University, was speaking to our reporter Peter Lloyd and a Papuan police spokesman contacted by PM says the two men have not been arrested and are free.