Marianne Kearney, Jakarta – Tomorrow, East Timor votes for its first president, taking its final steps towards independence.

It is a process that many in the Indonesian elite would probably rather forget but, of course, cannot.

Two years after an overwhelming majority voted for independence, many Indonesians maintain the fiction that a majority opposed it. This is part of a cynical attempt by the military to free itself of blame for human rights violations. The performance is primarily for domestic consumption.

Beyond this, the military and much of the political elite have not admitted how and why East Timor chose to be independent of Indonesia.

Although the military has blamed then-President B.J. Habibie for allowing a referendum, in fact, the only Cabinet member opposed to it in early 1999 was former foreign minister Ali Alatas.

Recent evidence shows the military was confident it could easily "persuade" the Timorese not to vote for autonomy. According to Australian intelligence, when Indonesian military leader Zacky Anwar Makarim was told that almost 80 per cent of Timorese had voted for independence, he was incredulous.

However, two years on, the Indonesian military has learnt little from the Timor experience, say analysts. In Aceh, it still believes military operations will ensure that the troubled province remains part of Indonesia. As in Timor, it has failed to see a link between the failure of the military to punish those guilty of abuses, and support for independence or autonomy.

There are progressive military figures, like the army deputy chief of staff, General Kiki Syanakri, who admits wiping out the rebel Free Aceh Movement (GAM) is impossible. He understands the importance of political negotiations. But there are also signs that the military still believes its own propaganda. And while there have been moves to introduce concepts of human rights into military and police training, observers say little has changed on the ground.

Perhaps the biggest lesson learnt from Timor was that Jakarta should never underestimate the dissatisfaction of Indonesia's outer regions. Now, there is no way Jakarta will allow Aceh or West Papua to hold referenda. But the vote in Timor and the reaction of the people in Aceh and West Papua have made Jakarta realise it has to offer more than just rhetoric.

The Timor experience added urgency to implementing autonomy for both Aceh and West Papua. West Papua's autonomy law is reasonably far-reaching. It is less so in Aceh. The Acehnese will be unable to elect politicians directly for five years.

And the government's introduction of syariah law in Aceh, an acknowledgement of the province's character, is being met with suspicion and confusion. Few Acehnese know how the law will be implemented. Even fewer have been consulted about it.

West Papua has a far more generous autonomy law, which involves traditional leaders in some government decision-making processes. But winning over Papuans, nearly all of whom support independence and who are ethnically, culturally and religiously different, could be harder.

Even if Jakarta understands the need to give Papuans control over their regional administration, is the chaotic and inefficient central government capable of delivering on its promises?