[Speaking for the first time, former Indonesian president B.J. Habibie tells David Jenkins how and why he made the fatal decision to leave control of East Timor in the hands of the military before the bloody referendum which secured the province's freedom.]

It is a golden summer's day in Paris and Dr B.J. Habibie, who served for 17 months as Indonesia's third president, has just left his serviced holiday apartment on the 34th floor of a tower block overlooking the Seine. The Eiffel Tower is a few hundred metres to the right, he points out, and you can just see it if you squeeze up against the window.

Not much further away is the Church of St-Louis-des-Invalides, where Habibie has spent the morning with his grandchildren, pondering the military and political career of Napoleon Bonaparte and coming to the conclusion that, on balance, Napoleon's achievements stack up less favourably than those of former President Soeharto.

Now, over a late lunch of consomme, omelet and salmon, Habibie is talking about East Timor, the province Indonesian critics say he had no right to "give away". Dressed in a khaki suit and string tie and sporting a post-retirement moustache, the former president is as ebullient and as voluble as ever – and keen to present his own version of those tumultuous events.

Habibie had been president for seven months when, in December 1998, John Howard wrote to him suggesting that there should at some stage be an act of self-determination in East Timor. The Howard letter was not especially welcome in Indonesia. But it does seem to have set Habibie thinking.

It reinforced the "let's ditch Timor" arguments being marshalled by his key advisers, many of them Muslim intellectuals who saw the largely Christian province as both mendicant and ungrateful, a burden being "carried" by the rest of Indonesia.

Within a month, Habibie had told his Cabinet he was willing to let East Timor slip the surly bonds of Indonesian control if that is what the people of the province wanted. The Indonesian army (TNI) had other ideas. It wanted to hold on to East Timor by fair means or foul. True to form, it opted for foul. In February, militia units recruited, trained, organised, armed, funded and fed by the TNI stepped up a campaign of terror against those favouring independence.

In the next seven months, 50 to 60 independence supporters were killed, many hacked to death with machetes as the army stood idly by. When the August 30 poll went so decisively against Indonesia, the militias went on an even more destructive rampage, killing hundreds and reducing much of the territory to a smoking ruin.

Why, many still ask, was there such a delay before an Australian-led force moved in to East Timor, on September 20? Why, for that matter, was a multinational force not in place when the poll was held? There were, Habibie says, two reasons – one internal, the other external – why he had refused to allow "Australian troops" into East Timor ahead of the UN vote.

"East Timor, with a population of 700,000 people, had been of interest to the world," he says. "But I had 210 million people. If I let foreign troops take care of East Timor, I will implicitly admit that the TNI cannot perform and it could be counterproductive for the stability of my whole country. And this risk I will not take." The army, he says, would have been seriously divided and quite possibly dangerous, with some military factions "playing politics" in a "very emotional and irrational society", jeopardising Indonesia's attempts to promote democracy. This first argument is persuasive. The TNI, angry about the referendum and engaged in a brutal covert operation designed to ensure a favourable poll outcome, would have felt humiliated by the arrival of foreign troops on Indonesian soil. Equally, Habibie's position would have been fatally weakened among the Indonesian political elite. With Indonesia refusing to budge on the issue, any multinational force would have had to fight its way in. No-one wanted that.

It would have meant sinking the Indonesian navy, shooting down the Indonesia air force and engaging in combat with the Indonesian army, actions that would have generated 100 years of enmity between Canberra and Jakarta.

In the event, Habibie put his faith – wrongly, as it turned out – in a TNI promise that it would guarantee security in the province, never imagining, it seems, that the Indonesian generals could be so mendacious, so callous, so obtuse and so incompetent, despite warnings that they could be all those things and more. The international community was obliged to do the same.

Habibie's second argument is less persuasive. Australia, he says, had been "a true friend" of Indonesia since the proclamation of independence in 1945 and he had had no wish to put that friendship at risk.

"I was convinced that if I let Australian troops come in to Indonesia, not only am I going to insult and embarrass the TNI, which would have been counterproductive for the other regions [of Indonesia], but if the Australians come in, whatever the decision will be, the loser would blame Australia.

"I am not going to take a risk that a people who are, in their hearts and their [deeds], real friends in helping us should [be brought] into a trap. That's wrong! ... I cannot let somebody help if they will be blamed. Cannot!" Nor, says Habibie, had it been possible to beef up Indonesian troop numbers in the province ahead of the UN vote, even though there had been concern about post-poll clashes between East Timorese.

Had he sent in additional troops a month ahead of the poll he would have created "an international problem because they will come to the conclusion I am preparing to ... sabotage the election. Difficult! If I let [too many] Indonesian troops come then they will say that I'm planning to win." To get around this problem, Habibie says he hammered out an agreement with UN Secretary-General Kofi Annan under which the UN would let him know the outcome of the vote three days before those details were officially announced.

Habibie argues that in those three days, Indonesia could have proclaimed a military emergency, withdrawn the TNI units then stationed in East Timor and replaced them with "new blood" – "disciplined" troops with no "cultural connection" with the territory and no sympathy for the integrationist cause. The new troops could have kept the situation under control "until the Australians arrived".

These plans came to nought, the former president claims, because Annan reneged on a promise to give three days' advance notice of the election result. Instead of giving Habibie three days' notice, the secretary-general had given him only 30 minutes' notice. Annan's announcement had triggered an "irreversible process" in which the province descended into anarchy.

"I thought I had three days. ... And then, I'm sorry to say, Kofi Annan said, 'I'm now on my way to announce that to the press.' And then we had the blow-up! ... You see! But of course I'm the bad guy!" Had the UN stuck by the agreement, says Habibie, repeatedly thumping the table for emphasis, "the amplitude of the destruction will not be 100 per cent as it was but maybe 10 per cent. The violence could be minimised ... we can prevent that happening." Asked whether he thinks Annan personally broke the agreement, he says, "If you get that [outcome, yes]. But I'm not going to blame him. Why should I have [a slanging match]?" That, he says, would achieve nothing.

"The United Nations, they have given their contribution, that the elections go fair. Why should I create unnecessary problems? But I think it is unfair, please, to blame all Indonesia." There is no doubt the UN did break its agreement with Indonesia, although the time frame was apparently two days rather than three. Habibie was to have been told the outcome of the poll on September 4, with the information only made public on September 6.

"I think it was a bad mistake to bring forward the announcement of the count," says a Western source with a detailed knowledge of those events. "It was done unilaterally.

"It looked at the time to be a dangerous gamble and it was. This was at a time when the UN was totally unprepared to cope with any violence. And they brought forth the likely outburst of violence. It was a stupid decision." The UN had argued, said this source, that the situation was getting out of hand, that there was mounting panic and that the East Timorese would be impatient or dissatisfied if they had to wait any longer; the uncertainty had to be brought to an end. "But it was unconvincing at the time and in retrospect, I think, it was a disastrous decision." Whatever the truth of the matter, it strains credulity to suggest that Indonesia could have withdrawn 14,000 soldiers from East Timor in two or three days and replaced them with a similar number of "disciplined" troops, "with UN experience", always assuming such forces could be found.

Jakarta was simply in no position to co-ordinate movements so that new troops were there before the old troops left. This would have looked like an Indonesian withdrawal, generating confusion and panic. "Rumours would have abounded," said one source. "'Indonesia has lost so they're withdrawing as quickly as possible.'" Nor can anyone be sure there would have been substantially less violence had the UN announcement been delayed. East Timor was tinderbox. The violence would presumably have broken out anyway.

About the best that can be said is that the UN would have had more time to make contingency plans.

Looking back, Habibie blames "criminal elements", not the TNI, for the violence that followed the poll. And much of the blame for that, he says, rests with the UN.

Asked who had been responsible for the killing and burning, Habibie says: "I don't know, I really don't. Amok! Amok! Uncontrolled and without any damper." Does he think the TNI Commander, General Wiranto, lost control of his troops? "No! No! Because he couldn't [do anything]. There's no decision announced. He couldn't march in." This, many would feel, lets Wiranto and his fellow officers off far too lightly.

Wiranto didn't need to "march in" to East Timor. He had 14,000 heavily armed troops there, including crack special forces units and members of the army strategic reserve, to say nothing of 8,000 police.

If Habibie seems to have put far too much trust in the TNI's pledge that it would guarantee security in East Timor and if he seems to be too inclined, even now, to exempt the TNI from any blame, he nonetheless wins praise from some Indonesia watchers.

"I think he performed a fairly honourable role [on East Timor]," says one source. "I don't think he lied at all. Whereas [Indonesian Foreign Minister Ali] Alatas often lied. But I don't think Habibie deceived anybody." Was Habibie surprised that 80 per cent of the people of East Timor voted for independence? "No," he says, "I was not surprised." The Timorese had never felt they belonged in Indonesia.

Looking at the events of 1999 from Western Europe, where he now spends much of his time, Habibie laments the bloodshed but takes pride in the fact that he was able to allow the Timorese their freedom, even though he had always been seen as an anak mas (favourite child) of Soeharto, the man who inflicted so much suffering on the territory. "Why," he asks rhetorically, speaking of himself in the third person, "is Habibie able to solve that and not Soeharto? Because if I saw that, I did not lose my face. I was not responsible for that [problem]."