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

But there's growing evidence that the squad is involved in torture and killings as parts of efforts by the Indonesian authorities to crush the separatist movement in West Papua. Reporter Hayden Cooper and producer Lisa Mayne travelled to West Papua to file this exclusive report. And a warning, this story contains graphic images.

HAYDEN COOPER, REPORTER: It's just after 9am on Thursday, the 14th June, and on this street in the Papuan capital, a killing is about to take place. The target is this man, independence leader Mako Tabuni, seen here speaking just weeks before his death.

VICTOR YEIMO, CHAIRMAN, KNPB: He is like my family. He is a martyr of revolution. He is the leader of West Papua. [inaudible] He is a good man.

ERSON WENDA, MAKO TABUNI'S RELATIVE (translated): We feel a very great loss because he was clearly a leader. The whole of Papua deplores that Mako was killed illegally. He was shot dead just like that, as if he was a thief.

HAYDEN COOPER: The killing by police left parts of the city in smoking ruins after riots broke out in protest. At his funeral, thousands mourned Mako Tabuni. His successor knows that he too is now in the firing line.

VICTOR YEIMO: The three days after Mako Tabuni's death they sent a text message to me. They said to me that "After Mako Tabuni is dead you are the next."

HAYDEN COOPER: You will be next?

VICTOR YEIMO: Yeah, I'm the next. I'm [inaudible] for us. It's already happened to us.

HAYDEN COOPER: Do you know where the message came from?

VICTOR YEIMO: I know that it's come from the Indonesian intelligence.

HAYDEN COOPER: The killing of Tabuni was a coordinated police effort. And 7.30's investigation in West Papua raises serious questions for Australia, because the funding and training provided by Australia for counter-terrorism now appears to be being used to crush the Papuan independence movement and assassinate its leaders.

We've come to West Papua to find out more about why Mako Tabuni was gunned down by police in broad daylight. And at this safe house on the outskirts of Jayapura, I'm about to meet two witnesses who are brave enough to tell us what they saw. Now, in both cases the men fear for their lives, so we've agreed to conceal their identities. But their accounts are compelling.

WITNESS (translated): As activists, we already knew this was a game played against us, and we have strong reason to believe that this is the work done by Detachment 88.

HAYDEN COOPER: Detachment 88 is the elite Indonesian police unit established in the wake of the Bali bombing, trained in forensics, intelligence gathering, surveillance and law enforcement by the US, the UK and Australia. They've played a crucial role in Indonesia's counter-terrorism efforts.

They're ruthless, often killing suspects. But their anti-terrorism mandate is now creeping into other areas, like policing West Papuan separatists - and human rights activists are concerned.

ANDREAS HARSONO, HUMAN RIGHTS WATCH: There is no doubt they are there in Papua. I believe that.

HAYDEN COOPER: This leaked video surfaced last year. It shows Detachment 88 after they reclaimed a remote air strip 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. It shows dead Papuans lying on the ground and appears to include picture of teenagers tied up with ropes.

Here is a more brazen show of force. It's the Papuan National Congress last October, when police opened fire on civilians. Witnesses say Detachment 88 was among the security forces that day.

GUSTAF KAWER, MAKO TABUNI'S LAWYER (translated): The fact is: Detachment 88 are in Jayapura.

HAYDEN COOPER: In 2009, Detachment 88 killed this militant Papuan activist Kelly Kwalik. He was a leader of the Free Papua movement, or OPM - a violent independence group with a record of attacking military and civilians.

The Papuan police chief praised the work of Detachment 88 in the killing, and later a WikiLeaks cable confirmed that a Detachment 88 team conducted the raid. But unlike OPM, Mako Tabuni's organisation KMPB says it is nonviolent, and instead pursue a political solution.

ERSON WENDA (translated): His way of fighting back was by doing interviews and press conferences. It was gentle. He wasn't violent. People say he had weapons and so on, but I was often at his house and never saw a pistol, and nor did my friends. We really don't believe it.

HAYDEN COOPER: Mako Tabuni's final day began here at this roadside food stand. A witness was with him and noticed several cars approaching.

WITNESS II (translated): As soon as they got out of the car they surrounded us. There were two of us, me and a friend and Mako in the middle. As soon as they got out, all the other people there disappeared and hid. So they came into the food stall and said, "Good morning, are you Mako? The police chief would like to see you."

HAYDEN COOPER: The men had arrived in unmarked cars and plain clothes. Tabuni ran.

WITNESS II (translated): He got free, he ran across the road, he ran about two metres alongside the taxi rank. 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.

HAYDEN COOPER: So this is the street where Mako Tabuni was shot. He came down here to buy some betel nuts to eat. A group of unmarked cars arrived; the police jumped out, tried to arrest him, he fled and they shot him right here on the left hand side. We can't get out and film here, because ever since then the police have been keeping a very close eye on what goes on around here, and especially on people who try to find out exactly what happened.

From here, Tabuni was thrown into the police van and taken - not to the nearby Catholic hospital - but to this police hospital at least 20 minutes away. This witness saw the authorities bring him in.

WITNESS (translated): He came in, I was shocked. I didn't know what had happened and it was a shock. They bought him in, and all they did was wash off the blood.

HAYDEN COOPER: This eyewitness says the police were from Detachment 88.

WITNESS (translated): I could tell, just from the way they looked. And when they bought him in, the people carrying him were wearing masks. There were two wearing masks, the ones who had hold of him, and they took him into the emergency ward.

HAYDEN COOPER: But Tabuni received no treatment.

WITNESS (translated): They washed off the blood and he could still talk so they took him to the police station for further questioning.

HAYDEN COOPER: But Tabuni received no treatment.

ANDREAS HARSONO: He was brought to the police hospital for one hour and a half. He was not treated properly, I think, and he died because losing too much blood.

HAYDEN COOPER: Tabuni's lawyer also blames Detachment 88.

(to Gustaf Kawer) What is it that leads you to suspect that Detachment 88 were involved?

GUSTAF KAWER (translated): 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. But they acted as if this was not an ordinary case; as if they were dealing with terrorists.

HAYDEN COOPER: Relatives agree it was Detachment 88 who killed Tabuni.

ERSON WENDA (translated): Clearly it was them who killed him, because we saw them shoot him and take him to their hospital.

HAYDEN COOPER: The Indonesian police report claims Mako Tabuni had a gun when he was shot, and that he grabbed another weapon from one of the officers. It also claims he was involved in seven violent offences before his shooting, but his lawyer says there's no evidence for any of the claims.

GUSTAF KAWER (translated): I think it's all a scenario created by the security forces so they could shoot him.

HAYDEN COOPER: Either way, Tabuni never got the chance to face the allegations against him. He was shot, according to witnesses, while running away.

GUSTAF KAWER (translated): They have to be put on trial. They can't just kill people. Those responsible for crimes against activists, those responsible for Mako's death, have to be investigated and dealt with in accordance with the law.

HAYDEN COOPER: To Papuan activists in Jayapura, Australia's support and training for Detachment 88 is galling.

VICTOR YEIMO: You give money for Indonesia to kill people in West Papua. You are the perpetrators... no, you are the... you are the actors of violence in West Papua.

HAYDEN COOPER: Mako Tabuni's death has sparked the attention of the Australian Government. On August 7th, diplomats in Jakarta raised concerns about the killing with Indonesia. Even so, it's little comfort to the independence leaders in this divided and dangerous province. They have little faith that the world really cares about their plight.

VICTOR YEIMO: Australian Government - also American government - they are actors of violence in West Papua because they fund them, they train them, and then with the gun they kill people. They kill us like animal.

The Australian Federal Police declined our request for an interview but you can read their written responses to our questions.

We had a written response from the Department of Foreign Affairs and Trade as well.

Foreign Minister Bob Carr did, however, give us an interview.

The Indonesian Government gave us a written statement.

And we also have some answers from authorities in West Papua:

Interview of Secretary of the province of Papua by 7.30

HAYDEN COOPER, REPORTER: Was Densus 88 involved in the murder of Mako Tabuni?

CONSTANT KARMA, SECRETARY OF PROVINCE OF PAPUA: What I know is that the police were at that incident but whether they were normal police or Densus 88 I don't exactly know, but there were police from Polda Papua there, the Papuan Police Force.

HAYDEN COOPER: Is any investigation being conducted into the death of Mako Tabuni?

CONSTANT KARMA: There is an investigation by Polda Papua and they are tracing in the police area.

HAYDEN COOPER: So the police are investigating?

CONSTANT KARMA: Yes, at that time there was observation by the Papuan Police.

HAYDEN COOPER: Are the Indonesian authorities taking strong action against the KNPB?

CONSTANT KARMA: There are actions being taken by local police against the KNPB because they have been doing things that the Government don't wish to continue.

HAYDEN COOPER: Is KNPB a violent organisation?

CONSTANT KARMA: Their principle is peaceful means but in reality they have also committed acts of violence.

HAYDEN COOPER: Have you ever seen Detachment 88 or been aware of them operating in West Papua?

CONSTANT KARMA: I don't really know about West Papua but in the Papuan Police (Polda Papua) there are also Detachment 88 on duty.

HAYDEN COOPER: What do they do in Papua?

CONSTANT KARMA: As far as I am aware, duties specific to the police.

HAYDEN COOPER: Are they involved in actions against separatist leaders or independence leaders or KNPB members?

CONSTANT KARMA: With the leader of KNPB, the man by the name of Buktar Tabumi, he was already arrested some time before the death of Mako Tabumi. He was already in the hands of the Papuan Police.

HAYDEN COOPER: Were Densus 88 involved in that?

CONSTANT KARMA: I don't know exactly know because it is a police headquarters, I don't exactly know the difference between the normal police, the Brimob and the Densus 88, I can't tell the difference, because they are all police.

Some images supplied by West Papua Media.