For several years stories have been circulating, mostly unpublished, concerning claims that Australian soldiers were engaged in acts of torture of militia prisoners in East Timor in 1999. All of those claims were dismissed by internal defence force inquiries but no details of the allegations or the evidence have ever been publicly available. Tonight, three militamen detail their experiences as prisoners of Australian forces.

Their story involves accusations of torture and the apparent disappearance of one of their fellow prisoners.

For the past fortnight we've been providing full details of these claims to the Australian Army. They've offered no denials to these claims and have refused multiple invitations to appear in this program. However late this afternoon, the Chief of the Army announced that an investigation would be launched.

Mark Davis: East Timor, September 1999. Australian troops are sent in to end the murder and mayhem of the pro-Indonesian militias and the Indonesian army, and end it they do. The operation was a great success and the Australian army readily accepted the well deserved applause.

John Howard, Australian Prime Minister: Congratulations and thank you very much for the fantastic job you've done.

But are they as willing to accept responsibility for the darker corners of the mission. At the time, stories were circulating in Indonesia that Australian soldiers were torturing and even murdering prisoners. Reports dismissed here as ludicrous propaganda, but apparently not entirely ludicrous to some within the Australian, British and New Zealand armies who witnessed and reported certain undisclosed events.

Virtually unknown to the Australian public, the Australian Defence Force, the ADF, conducted an investigation for 3.5 years into allegations of mistreatment of prisoners in East Timor, including torture, execution and one case of unnecessary amputation.

In April of this year, the ADF called a press conference in Canberra to suddenly announce that undisclosed allegations had been found to be unsubstantiated.

Canberra press conference: All of the time they were treated properly and correctly under the Geneva convention.

End of story according to the Defence Department.

Senator Chris Evans, Shadow Defence Minister: Mr Chairman, could I ask some questions about this military investigation into the allegations of mistreatment of prisoners in East Timor?

Army Officer: Senator, the investigation concluded and I announced the results on 16 April.

In June, at a Foreign Affairs and Defence Senate committee hearing, Chris Evans sought further details about the allegations and the processes of the inquiry without much success.

Evans: Just trying to be clear in my own mind. The ADF admitted last year the allegations were of a serious nature, allegations of torture and abuse of prisoners. So these are the most serious allegations and obviously there's the allegation concerning the kicking of a body. Now those are most serious. They really besmirch the reputation of the SAS and ADF generally and they need to be dealt with properly. Until that time, all ADF personnel have their reputations besmirched by the fact these allegations haven't been answered.

It was clear that not even a Senate hearing would be privy to the details of the allegations. There's never been a full explanation of how the internal investigation was conducted, how the evidence was judged, who was interviewed and why the claims were dismissed.

Evans: You announce on behalf of ADF that unspecified allegations are found not to be proven and that's it.

Neither the ADF or the Defence Minister, Robert Hill, would appear in this program to explain or defend the army inquiry. But working through a handful of terse press releases, the inquiry has the appearance of being little more than defence force investigators interviewing defence force witnesses to be judged internally by defence force officers. Of 18 allegations involving East Timorese prisoners, only one received any public prominence, an offence of kicking a corpse, which was to be sent to trial.

Army officer: As a result of the investigation, one serviceman has been charged with kicking a dead body and the matter was referred to a convening authority who has decided that the defence force magistrate should try that.

That single charge involving the SAS, was dismissed in August when key witnesses from the New Zealand army refused to attend the trial. A refusal which goes to the heart of the problem of soldiers investigating soldiers.

Evans: The culture of the ADF is to not to share information about these matters. The culture is to say these are internal matters that have to be kept in-house. I don't think that's acceptable.

These are the most serious allegations and issuing a press release every now and then when the matter bubbles to public attention, which gives the minimum information possible, is not acceptable. It's just not good enough. We do need much better information and we do need a full explanation of these most serious allegations and what happened and what was done to follow them up. Because without that, this will continue to be a blight on the ADF and there'll continue to be allegations raised in the years to come. It won't go away.

The army has provided no information about whether they talked to any victims from East Timor at all.

That is what we asked East Timorese journalist Jose Belo to do. Jose spoke with Jao Ximenes, now a fisherman in Dili. In September 1999, Jao was arrested with five other suspected militiamen, although he denies he was a member. Today the only sign of his alleged mistreatment is a smashed toe, deliberately crushed, he claims, under the heel of an Australian soldier during interrogation.

Joa Ximenes, (translation): They forced us to go into the toilets, which were full of wasps. They stirred up the wasps and they stung us. Then they took us to the toilet bowl and they put our faces inside again.

He also claims that one of his fellow prisoners has never been seen again. To verify his story, we searched for and found two of his fellow detainees, now living in Indonesian West Timor.

Caetano da Silva, (translation): My name is Caetano da Silva. I am 38 years old.

Caetano was a member of the notorious Aitarak militia, arrested and interrogated with Jao and now living in the Indonesian town of Kupang.

Johnny Rohiede, (translation): It was inhumane. We were told to lie down on human faeces. They hit us. They say Westerners are never cruel. But they abused us, hit us, mistreated us.

Johnny Rohiede was a driver for Aitarak, now living in Atambua in West Timor. Both he and Caetano confirm Jao's account. They didn't come forward to us with any collective statements. We tracked them down in their homes and interviewed them immediately. Their stories closely match in virtually every important detail.

The Aitarak militia, led by Eurico Gutteres, were one of the most infamous and violent of all the militias in East Timor accused of involvement in acts of murder and mutilation. There would be few who would harbour any sympathy for any Aitarak member. We do not know what the witnesses were suspected of. The only known factor is that they were prisoners at the mercy of the Australian army, who presumably, unlike the militias, are expected to operate with the highest standards of the discipline and integrity.

Rohiede, (translation): They interrogated us again but it was more like torture. When they started hitting us they did not punch us like this. Not like this, like this. And they kicked us with the soles of their feet. Why? So there? be no bone damage if we were examined, just normal bruising. That? how Westerners think.

It was here at Aitarak headquarters where Jao and the others were arrested by Australian soldiers on September 22. Jao recalls five of them being arrested here.

Rohiede, (translation): Luis Heru, myself, Johnny Rohiede7

Johnny recalls six being arrested but in all other respects, their accounts correlate.

Rohiede, (translation): Caetano da Silva, Lorenco Gomes, Joa Ximenes, Yani Ndun. Of these six, only Yani is still missing.

All of the witnesses state that Yani Ndun, a native of West Timor, was arrested with them. Apart from some robust handling, there are no particular accusations of mistreatment at the time of their arrest. But that changed when they were taken inside the more private environs of the Dili football stadium. The Dili football stadium became well known to Australian audiences as an R and R destination for soldiers in East Timor. Before that, it seems it was a primary interrogation centre for the captured militiamen. At the rear of the stadium, in an unused corner, is the room where the militiamen were taken.

Joa Ximenes, (translation): Here. This is it. It? still dirty like it was then. It's still not clean. The five of us were all in here. It's still the same. The shit is still here. Their nests were this big. The wasps were big too. Big red ones. The wasps were this big. All five of us were badly stung and we were in bad shape.

Jose Belo, Timorese journalist, (translation): Show me where did you go?

Joa Ximenes, (translation): We went in here, one person at a time. They put our heads in the toilet bowl. Into the toilet one at a time. One person at a time, with their mouth down the toilet.

Jose Belo, (translation): Were your faces dipped in the shit?

Joa Ximenes, (translation): Yes, covered with shit, the worst kind. The shit is still here. They made us put our mouths here. If we tried to pull away they pushed our necks down to stop us moving.

Jose Belo, (translation): Do you know which foreigners?

Joa Ximenes, (translation): Foreigners from Australia because of their badges. Yes Australia.

Jose Belo, (translation): The men who beat you up were Australian?

Joa Ximenes, (translation): Yes.

Jose Belo, (translation): Do you know their names?

Joa Ximenes, (translation): No, I don't. I just saw their badges.

Caetano and Johnny both confirm the account of this stage of their treatment and each of them maintain they were beaten in the hours to follow.

Rohiede, (translation): Bruises on the back, swollen here, and bruised here when they hit me on the tennis court.

For the past fortnight, despite being provided with full details of these allegations, the ADF has issued no denials or defences other than maintaining that the prisoners would have been kept in accordance with the Geneva convention. They had no response to any of the testimonies we provided them with.

Andrew Byrnes, Centre of International and Public Law, ANU: They're very serious allegations and I imagine the defence forces would want to investigate them vigorously.

We asked international law specialist Andrew Byrnes from the Centre for International and Public Law at the ANU to scrutinise the statements.

Andrew Byrnes: There is a certain detail, a concreteness in the allegations which has, I think, the ring of truth about it when you look at the other sorts or similar sorts of allegations made by victims, there are a number of consistent patterns from the various stories, we don't know whether there's collusion, there's no suggestion that there is but where you get consistency in stories about particular methods, then I think that should certainly alert one to a higher level of credibility.

After their experience at the stadium that evening, the prisoners were taken to the tennis courts at the local high school.

Caetano da Silva, (translation): They threatened me saying "if you don't say which soldiers or police killed people, you will be killed."

Jose Belo, (translation): Who asked all these questions?

Caetano da Silva, (translation): Australians.

All of the three witnesses maintain that Yani was still with them at the tennis courts and that he had been with them at the football stadium.

Rohiede, (translation): Yani, the guy who disappeared, was a bit crazy. We all knew that at times he'd go mad. It was an illness he'd had since he was small. Because he was mad, when Interfet came in with their rifles cocked he said "mister, smoking". They weren'tmad at him, they hit me. I got hit the most.

It was at the tennis courts that Johnny and Caetano last saw Yani and none of his friends or family have seen him since.

Caetano da Silva, (translation): They hit us and kicked us every time we moved. At about 2.30 or three o'lock they brought us out and they blindfolded us and when I saw them with a bag, the kind they use for executions, I wondered if they were going to kill us.

Blindfolded, the prisoners were driven to Dili airport, then serving as an interrogation centre and prison. Both Caetano and Johnny believe that Yani may have been removed from the vehicle on the way to the airport. But Jao believes he caught a glimpse of him there before they were all separated. In any case, it seems that no-one has caught a glimpse of him since.

Rohiede, (translation): After a week when people started coming back, he didn't. They went to 13 districts just to look for Yani. They didn't find him so they came back. They said "we can't find Yani, we've been to 13 districts, he's not there."

Jao maintains that he was the last prisoner released from the temporary airport prison as he told the others when they came searching for Yani.

Joa Ximenes, (translation): I said "I thought the four of you were together." He said "No only three of us left and we thought he stayed with you." I said "I was the last to leave."

Jose Belo, (translation): So in your mind Yani was dead?

Joa Ximenes, (translation): I thought he was dead because I hadn't seen him. His family hadn't seen him either.

The ADF have records of arresting and releasing other members of the group, but no records whatsoever relating to Yani Ndun. His family, who don't wish to be filmed, say they saw him on Indonesian television being arrested at Aitarak headquarters with the others and he's never been seen since.

Andrew Byrnes: I think it's very clear under international law that where state forces take someone into custody, and then they are not able to be produced subsequently, that that state does have a responsibility to explain what has happened to the best of its ability. Now that may...

With no response from the army, it's difficult to speculate on Yani's fate. If he was arrested and is now dead, it may possibly be at the hands of others if he was released on the streets of Dili after the Indonesians had gone, then a very dangerous place for a militiaman with no family in East Timor.

Andrew Byrnes: If someone were released into a circumstance where the people releasing him knew that his life would be subject to immediate threat or they would be at risk of being lynched by a mob, that that would give rise to liability on the part of the releasing force.

There may yet be an explanation offered for the disappearance of Yani, and hopefully some response to the allegations of torture. The responsibility for both ultimately lies with General Cosgrove as the commanding officer of the East Timor operation and in his current post as chief of the defence forces.

Rohiede, (translation): If they violate human rights, punish them just like the Indonesians. If I get protection I'll go and point them out.

Senator Chris Evans: And that leaves the whole thing basically up in the air.

If there is an inquiry, and if the procedures followed for the previous 18 allegations are a guide, we may never hear any details of it, nor how it was conducted, nor who was interviewed, nor if the evidence of victims will carry any weight against the evidence of soldiers and officers.