An elite counter-terrorism unit trained and supplied by Australia is being accused of acting as a death squad in Indonesia's troubled West Papua region.

The group, known as Detachment 88, receives training, supplies and extensive operational support from the Australian Federal Police.

But there is growing evidence the squad is involved in torture and extra-judicial killings as part of efforts by Indonesian authorities to crush the separatist movement in West Papua.

The AFP were contacted by 7.30 and outlined their involvement with Detachment 88 - read here.

Read the Indonesian Government's response to the 7.30 coverage here.

The ABC's Hayden Cooper and Lisa Main went undercover in West Papua to meet with many who say an Australian Government-funded anti-terrorist team is waging a bloody campaign against activists.

On June 14, popular independence leader Mako Tabuni was gunned down as he fled from police on a quiet street in the Papuan capital.

The men who killed Mr Tabuni, was was deputy chairman of the National Committee for West Papua (KNPB), were allegedly part of Detachment 88.

Trained in forensics, intelligence gathering, surveillance and law enforcement by officials from the US, the UK and Australia, the unit was established in the wake of the Bali bombings and has played a crucial role in Indonesia's counter-terrorism efforts.

They are ruthless, often killing suspects, and their anti-terrorism mandate is now creeping into other areas like policing West Papuan separatists.

In December 2010, Detachment 88 killed militant Papuan activist Kelly Kwalik.

Mr Kwalik was a leader from the Free Papua Movement (OPM), a violent independence group with a record of attacking military and civilians, and Detachment 88 publically claimed responsibility.

'Gentle way'

But KNBP's current leader, Victor Yeimo, say unlike OPM, KNBP is non-violent and instead pursues a political solution.

Mourners during the funeral of West Papuan independence leader Mako Tabuni ( Papua Cooperation Forum: AFP )

"Mako was a good man. If someone was angry, Mako wouldn't answer them," he said.

"Even if people were angry, if he was being questioned by the police, they'd speak to him but he'd just laugh.

"His way of fighting back was by doing interviews and press conferences, it was gentle.

"People say he had weapons and so on but I was often at his house and I never saw a pistol and nor did my friends."

According to eyewitnesses, after being approached by plain-clothed police in unmarked cars, Mr Tabuni attempted to flee.

The witness said police opened fire on the activist as he ran down the road.

"He got free, he ran across the road, he ran about two metres alongside the taxi rank," one witness said.

"He ran along the taxi rank and tried to climb down into a gully, a drain, under the bridge.

"He was shot in the leg, he was shot but still tried to escape, then they shot him in the torso."

Bleeding heavily, Mr Tabuni was taken not to the nearby Catholic hospital, but to a police hospital at least 20 minutes away, where another witness saw the authorities bring him in.

"When he came in, I was shocked. I didn't know what had happened and it was a shock," he said.

"They brought him in and all they did was wash off the blood."

'No evidence'

The man says the police were from Detachment 88, based on their distinctive masks often worn in operation.

"I could tell just from the way they looked. And when they brought him in, the people carrying him were wearing masks," he said.

Gustaf Kawer, Mr Tabuni's lawyer, also believes Detachment 88 was involved.

"They used an ordinary car and also a ute. Usually, when the police make an official arrest they wear police uniforms and use police vehicles," he said.

"But they acted as if this was not an ordinary case, as if they were dealing with terrorists."

The Indonesian police report claims Mr Tabuni had a gun when he was shot, and that he grabbed another weapon off one of the officers.

They also claim he was involved in seven violent offences before his shooting.

But Mr Kawer, who is respected internationally, says there is no evidence for any of the claims.

"I think it's all a scenario created by the security forces so they could shoot him," he said.

"At the present time the police are only holding two of the people who are alleged to be involved with him. They're still being held by the police.

"Witness testimony points to their being involved but there's not enough evidence against Mako."

Without restraint

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Watch Duration: 13 minutes 55 seconds 13 m Rare look inside West Papua independence movement ( Hayden Cooper )

The activist's death is just one of many examples of Detachment 88 operating with impunity.

A leaked video surfaced last year showing Indonesian police after they had reclaimed a remote airstrip from militant separatists.

The trophy video, taken on a mobile phone by the police, identifies Detachment 88 officers, who are often embedded with other units, and dead Papuans lying on the ground, including pictures of teenagers tied up with ropes.

And witnesses say Detachment 88 was among the security forces that opened fire on civilians at the Papuan National Congress last October.

To Papuan activists like Mr Yeimo, Australia's support and training for Detachment 88 is galling.

"You give money for Indonesia to kill people in West Papua - you are the perpetrators of violence in West Papua," he said.

"[The] Australian Government and American government, they are actors of violence in West Papua.

"Because they find them, they train them and then with the gun they kill people, they kill us like animals."

Mr Tabuni's death has sparked the attention of the Australian Government, with diplomats in Jakarta raising concerns about the killing with Indonesia on August 7.

And the Federal Government says it is asked Indonesia to conduct inquiries into human rights abuses and killings in the province of Papua.

Foreign Affairs Minister Bob Carr says he does not know if the reports are true, but he says he has spoken with his Indonesian counterpart, Marty Natalegawa, about the issue.

"Well we think the best way of clarifying the situation is for an inquiry. We've never hesitated to raise human rights issues in the two Papuan provinces and we'll continue to do it," he said.

But Australia's response is little comfort to the independence leaders in the divided and dangerous region.

Mr Yeimo says his people have little faith that the world really cares about their plight.

"The world is behind Indonesia now, it means they all compromise with Indonesia to kill West Papuan people," he said.

And he knows that he too is now in the firing line.

"The three days after Mako Tabuni was killed by Indonesia, they sent a text message to me, they said to me that 'after Mako Tabuni's dead, you'll be next'."

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Watch Duration: 5 minutes 50 seconds 5 m Bob Carr responds to West Papua accusations

Statements from the Australian Federal Police and Indonesian Embassy below: