John Mcbeth, Senior Writer – Even the commissioners themselves privately acknowledge that there is one thing missing from the hearings conducted by the Timor Leste-Indonesia Truth and Friendship Commission into the bloodshed surrounding Timor Leste's 1999 vote for independence. And that is the truth.

When the commission finally releases its report in January, it is not going to be some sort of panacea. Not by a long chalk. After all, the 10-person body has no legal basis and was devised by politicians as a coldly pragmatic way for both countries to try to get the past behind them.

It will certainly never satisfy the families of the 1,400 people who died when military-backed gangs laid waste to the province before and after the UN-sponsored referendum that ended 25 years of brutal Indonesian rule.

It will not satisfy the United Nations either. When refusing to allow his officials to testify at the hearings, UN Secretary-General Ban Ki Moon said that the organisation "cannot endorse or condone amnesties for genocide, crimes against humanity, war crimes or gross violations of human rights, nor should it do anything that might foster them".

Indonesian Foreign Minister Hassan Wirajuda criticised the UN's decision to boycott the hearings, but really it is like two ships passing in the night – with their radars functioning perfectly and their positions picked out with spotlights.

Under these circumstances, no one is going to tell the truth, even if they wanted to. Certainly not some of the leading figures, who have no guarantee that their "confessions" will not turn up in the case files of a future UN human rights tribunal – as unlikely as that appears to be now.

Some critics feel the UN raised the bar too high from the outset. But for Indonesian military officers, what constitutes the truth will forever be coloured by their conviction that what they did was right. They do not want to be forgiven.

Rather than acting as an attorney, the commission will be basing most of its conclusions on what one member describes as "scientific research". He says that the five public hearings it has held so far in Bali and Jakarta are only being used for transparency and public relations purposes. As he noted: "In terms of substance, we don't get much out of it. We can't expect those involved are going to give evidence according to our wishes."

The commission has yet to decide whether it will recommend amnesty or not for those accused of gross human rights violations. If it does, the give-and-take mentality required of the commissioners means they are likely to adopt a holistic approach rather than focusing on individual cases.

"Recommending amnesty is not mandatory, but it is one of the instruments that could be used by the commission to carry out its mission," says one insider familiar with its deliberations. "It may be a non-judicial body, but it still has the freedom to use amnesty in the implementation of its mandate."

The commission is working with four sets of documents – the Indonesian Human Rights Commission report on Timor Leste, the transcripts from Indonesia's ad hoc tribunals, Timor Leste's Reception, Truth and Reconciliation Commission (CAVR) report as well as testimony given to the UN Serious Crimes Unit.

The Indonesians are anxious for the events of 1999 to be seen from a 2007 perspective, but it does not help that the military is now back to promoting some of the officers accused of human rights abuses in Timor Leste and Indonesia.

Take, as an example, Jayapura district commander Colonel Burhanuddin Siagian, who was indicted by the UN Serious Crimes Unit in 2003 for murder and torture when he served as commander of Bobonaro district on the East-West Timor border.

Col Siagian allegedly oversaw the creation of the best-developed anti-independence militia system in Timor Leste. Human rights activists have seized on this as evidence that he is now doing the same in Papua.

His threats have not helped. "Anyone who uses the state's facilities but who still betrays the nation, I honestly will destroy him," he was quoted as saying on May 12 after students called for a review of the long-criticised 1969 Act of Free Choice, which placed Papua under Indonesian rule.

Why send the colonel to Papua of all places when he could just as easily been given a comfortable sinecure out of harm's way in Java? It almost seems the army is doing this for no other reason than to demonstrate its defiance. It is not a nice look for an infant democracy trying to put a culture of impunity behind it.