In a few days the taxing, unenviable job of the men and women tasked to dig up the truth about violence around the time of East Timor's 1999 referendum should be over.

Well past its earlier, already extended deadline of January, the Indonesia-Timor Leste Commission on Truth and Friendship (CTF) should submit its report shortly to the presidents of both countries.

The hurdles to their task, widely expected by the public and no less by the commissioners themselves, have persisted to the end.

Last week the deputy chairman for Indonesia, Agus Widjojo, said the joint commission had to come through "a tough process to seek consensus" before they could submit the report.

Since both countries agreed to set up the commission in 2005, the label "mission impossible" has stuck, for it is unique and probably a world first of its kind. Two countries, the Goliath with over 200 million people and the tiny David of 1 million, which the Goliath formerly occupied, were supposed to work together and come up with the truth of very recent violence, and make up and put everything behind them.

The logic was clear. A newly independent Timor Leste desperately needed its "big brother" for its survival and growth, despite animosity accumulated mainly from brutal treatment of its neighbor's military and New Order regime under Soeharto, Timorese citizens and activists had said. Many Timorese were resentful of their leaders' pragmatic decision to seek a solution through the set-up of the commission.

Also loud and clear were, and are, the problems against investigating the "truth". One problem is that Indonesians have never seen themselves as the former "occupier" of East Timor – even as Timorese commissioners quietly ask whether the Dutch can ever erase their historic trademark as our former colonialists.

Another may relate to the fact that when you've denied problems for so long you tend to believe your own justifications and reasoning.

This was clear in a few public hearings of the commission featuring retired Indonesian generals. Former Indonesian Military chief Gen. (ret) Wiranto was among those who said the chronic violence in Timor Leste could be traced to the local culture of violence. It was the only way those poor people understood.

Part of the general's audience found it hard to keep a straight face at such a simplistic conclusion, but the repeated applause from his supporters would not be limited to only a few among the Indonesian public.

Just look, such people would say: Since their independence we have not seen the Timorese able to enjoy peace for long. Dili alone still has tens of thousands of refugees, not to mention some 10,000 displaced people along the border with one of Indonesia's poorest provinces, East Nusa Tenggara.

Indonesians smirk at Timor Leste's continuous inability to preserve stability, the latest incident ending in the shooting of President Jose Ramos-Horta. The country remains poor and violence-ridden, surely in a worse state than the days of the benevolent Indonesian Republic.

What many Indonesians cannot fathom is what drove Timorese to overcome all their fears and come out and vote in the 1999 referendum that led to their independence – and why they won. But worse, the issue is rarely even questioned.

So what could the commission possibly achieve? Can it educate Indonesians and Timorese, can it nudge painful realities under the noses of those who refuse to see?

If indeed there are ugly facts, will President Susilo Bambang Yudhoyono tuck the report under his arm and hope we will all forget, as he did with an earlier report of another commission he appointed himself, the fact-finding team on the murder of the activist Munir?

Commissioners have repeatedly said they "can't satisfy everyone", for their mandate is neither for the prosecution of individuals considered guilty, nor the rehabilitation of victims.

They said the report will name "an institution" responsible for the 1999 violence, seek "lessons learned" and establish whether there were "gross crimes against humanity".

Indonesia's credibility in the international community won't increase much if the report fails to pinpoint anything with clarity. Timorese may shrug and get on with their long struggle for peace and prosperity. They already had their outpouring of admittance and tears through their own commission on truth and reconciliation.

But it is Indonesians who stand to lose the most if the CTF, or our leaders, choose to gloss over the facts and treat all the destruction and violence in Dili and other towns as mere tragic "excesses" of a virtual power vacuum in the days before and after the 1999 vote.

Time may heal the Timorese' pains. But we will continue to be blind over our history.

The CTF is not tasked with handling the entire chapter of Indonesia-East Timor relations. But failure to tackle merely the end part of that past will make it increasingly hard to answer our grandchildren's query: "If you were so kind to East Timor, Grandpa, why did they want to break free?"