Richard LLoyd Parry Blog – It is a law of guerrilla wars that they are morally murky affairs, in which it is impossible to separate right from wrong or to sympathise unconditionally with either side. The British Army and the IRA in Northern Ireland; the Serbian state and the Kosovo Liberation Army; the US-Iraqi government against the Sunni insurgency – wherever your sympathies lie, only a partisan or propagandist could fail to see cruelty and stupidity on both sides. I know of only one exception to this rule in my own experience: the 24-year struggle between the East Timorese guerrillas and the occupying army of Indonesia.

East Timor was that rare thing: a morally black-and-white conflict. Partly, this was because of the circumstances – the Indonesian invasion of 1975, after the abandonment of the territory by colonial Portugal, was a straightforward case of international thuggery. Partly, it was because of the winking collusion of governments which should, and did, know better, including Britain, the United States, and Australia.

But it was also because of the discipline and restraint of the East Timorese resistance, the guerrilla army called Falintil. Before their skulking withdrawal in 1999, the Indonesians employed the nastiest tricks in the counter-insurgency manual: napalm, hamletting, the bombardment of civilians, mass deportation, torture, rape, and extra-judicial execution. Two hundred thousand people, by the commonest estimate, died of violence, disease and starvation. But, with the rarest of exceptions, the guerrillas met Indonesian brutality with outstanding decency and restraint.

Falintil was overwhelmed. It had a few old Portuguese rifles and no heavy weaponry. But it never resorted to the terror tactics of guerrillas elsewhere in the world. The victimisation of civilians, the lynching and knee-capping of informers, the bombing of Indonesian cities – none of these were ever a feature of the war in East Timor. Even after the violence of September 1999, when the Indonesian army burned the country in retaliation for the country's vote for independence, there were no serious reprisals. Much of the credit for this lies with Xanana Gusmao, the guerrilla leader and former political prisoner, who is now the first president of his independent country.

But now I wonder whether Xanana's restraint is going too far.

Last week he submitted to the East Timorese parliament a report by the Commission for Reception, Truth and Reconciliation in East Timor (CAVR), an independent organisation established by the East Timorese government. The report has taken more than three years to compile. It is 2500 pages long and draws on the testimony of 8000 witnesses. Its authors include a businesswoman, a Catholic priest, a Protestant clergyman, an aid worker, a human rights activist, a former political prisoner, and a former civil servant in the Indonesian administration who opposed independence – as wide and balanced a cross section of experience and opinion as one could hope to find in a small, poor, new country. The CAVR report, in other words, it is the closest thing to a definitive account of East Timor's suffering as anyone has yet produced.

But President Gusmao has so far refused to publish it, for the simple reason that, having struggled against them for 24 years, he does not want to offend the Indonesians.

The report's recommendations, which I have seen, are strong and startling. They include the setting up of a reparations programme for victims of the conflict, to be funded not only by Indonesia, but also by the foreign governments, and their arms dealers, whose complicity allowed the invasion to run so smoothly.

The commissioners call for Indonesians suspected of crimes to be handed over to East Timor, and for criminal investigation of the entire period from the invasion in 1975, not only the end of the occupation in 1999.

Now these are grave diplomatic actions, not be undertaken lightly. Indonesia literally surrounds Timor. It is, and always will be, the country's greatest trading partner, and cultural and political influence. Having come to their senses in 1999, western governments are doing much to help East Timor.

"For me and for my president and my government as a whole, it is out of the question that we would even raise this issue with these countries," said Jose Ramos-Horta, East Timor's foreign minister and winner of the Nobel Peace Prize. "We will not. It would be undiplomatic. It would not be fair. It would be showing lack of gratitude, lack of statesmanship, lack of maturity."

And yet the alternative is worse, and spelled out clearly in the CAVR report. "Impunity has become entrenched," it declares. "Those who planned, ordered, committed and are responsible for the most serious human rights violations have not been brought to account, and in many cases have seen their military and civil careers flourish as a result of their activities. Respect for the rule of law and the organs of the state responsible for its administration, a fundamental pillar of the democratic transition in Indonesia and nation building in Timor-Leste, will always be extremely fragile in this context."

"My reply to that," Xanana said in a bizarrely long-winded speech, as he reluctantly presented the still secret report to parliament last week, "would be 'not necessarily'."

Xanana Gusmao is the last person I have been able to think of without hesitation as a hero. I hesitate to question his sincerity, and in plenty of ways, East Timor has been lucky to have a leader so unconventional, decent, and forgiving. But how depressing to hear such a man speaking in the cant of the invaders he fought so long to drive away.