BELATEDLY, Indonesian President B. J. Habibie has spoken some important truths to his nation's parliament. The people of East Timor voted overwhelmingly to become independent of Indonesia; "we must honor and accept that choice," Mr. Habibie said yesterday. Many Indonesians will find his advice difficult to accept. The news that 80 percent of East Timorese want independence has stirred nationalist resentment in Jakarta and elsewhere. For decades, after all, Indonesia's government-controlled media insisted, under President Suharto's dictatorship, that East Timorese were happy with the status quo. As Mr. Habibie acknowledged, "For a long time, consciously or not, we have offered to our nation a version of reality that was not truly being experienced." As Indonesia democratizes, it's harder to maintain such official deception, and other political leaders -- including presidential hopeful Megawati Sukarnoputri -- have a responsibility to speak honestly, too.

The president's statement, and his tardy acceptance of a U.N. force that is now establishing itself in East Timor, are important steps. But they are hardly sufficient. The Aug. 30 referendum was followed by a wave of violence against the civilians of East Timor by anti-independence militias, which were abetted and encouraged by Indonesia's military. Much of the capital of Dili was destroyed, and even now more distant villages are burning. Although a vanguard of Australian and other troops has entered Dili, hundreds of thousands of people are hiding in the mountains, afraid to come home and vulnerable to militias and to disease.

If President Habibie really wants "to finally resolve the East Timor problem in an honorable manner," as he urged yesterday, he should order the Indonesian military to fully withdraw so that East Timorese can dare to return to their ruined houses and begin to rebuild. His government should allow humanitarian agencies access to refugees who were forced into West Timor, which remains under Indonesian control, and should allow those refugees to go home. Indonesia also should cooperate with the United Nations in investigating the crimes against humanity that took place during the past few weeks, and in holding accountable those responsible. And Mr. Habibie and other Indonesian political leaders should make clear that Australia, a current focus of nationalist anger, is performing a brave and necessary job. Indonesia's military not only proved unable to maintain order in East Timor; the armed forces were heavily responsible for the mayhem. Mr. Habibie and other would-be presidents should be saying that, too.

Some diplomats argue now that the United Nations should ease off on such demands so as not to injure Indonesia's democratization. But confronting history honestly, as Mr. Habibie yesterday began to do, and respecting East Timor's democratic wishes can only enhance Indonesia's own democratic aspirations. Appeasing Indonesia's darker, nationalist forces will not push the country in a positive direction.