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 Indonesia's disputed Papua province.

Activists says 11 people were killed and 20 more are missing after a combined military and police crackdown on support for the Free Papua separatist movement in April.

The names of victims and several grisly photographs have been provided to ABC's PM by the armed wing of the movement.

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

Indonesian police say the claims are untrue. The Papua police spokesman, I Gede Sumerta Jaya, says the killings did not happen and that unit does not operate in the Papua provinces anymore.

The disputed Indonesian Papua province is the least populated but most restive corner of Australia's vast near neighbour.

For 50 years Papuans have agitated for independence from their Javanese masters in a campaign fought bitterly 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 is from this territory that the shocking claims of extra-judicial killings are emerging.

The ABC conducted an interview with the spokesman for the military wing of the Free Papua organisation, Jonah Wenda, via an exchange of text messages after telephone communications failed.

He said that an entire village was targeted.

"Indonesian government fear this village is a strong hold of Freedom Fighters in the centre highlands of West Papua," he said.

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"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 through in the river."

Mr Wenda emailed the names of the 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 said there were two instances of rape.

None of the 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.

Killings account accords with growing intimidation

Professor Damien Kingsbury from Deakin University has been studying the decades long struggle by the Indonesian state to exert its will over the Papua province.

He believes the claims of a mass killing are consistent with an upswing of violence and intimidation across the province.

"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," he said.

"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."

He says the violence is being fuelled by increasing separatist intent.

Papuans have agitated for independence from Indonesia for decades in a bitterly fought campaign. ( ABC TV )

"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," he said.

"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 police are cracking down on it."

Professor Kingsbury says it is possible residents of one particular village are being targeted for showing sympathy to separatist sentiment.

"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 primarily execute," he said.

"I think this is the nub of the problem in West Papua, that he 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.

"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."