Five thousand supporters of independence turned out at the gathering, after a much smaller rally on Saturday by about 600 of their opponents who favour the other option being presented in the referendum: limited autonomy within Indonesia.
The weekend's events mark the beginning of the final and most perilous phase of the fraught referendum process before voting itself takes place on 30 August.
The green, white and blue flag was raised to mark the re-opening of the offices of the National Council for Timorese Resistance (CNRT), many of whose leaders have been in hiding since anti-independence militias began a campaign of killing and intimidation earlier this year.
In a speech recorded from house arrest in Jakarta, Jose "Xanana" Gusmao, the leader of the East Timorese guerrilla army, Falintil, urged his supporters to avoid violence against supporters of Indonesia. "I hope for a campaign of peace," he said. "Now is the time for East Timorese to determine their future. For the past 24 years our enemy has not been the East Timorese people who want integration with Indonesia. Our main enemy has been the Indonesian military."
Despite the indignant denials of the Indonesian government, foreign observers - including the United Nations' mission which is supervising the referendum - have been unanimous in concluding that the militias are the tools of the Indonesian military.
Last week, Jimmy Carter, the former United States president, said that "the Indonesian military and other government agencies are supporting, directing, and arming pro-integration militias to create a climate of fear and intimidation". The US State Department accused Jakarta of intimidation for encouraging fears that the referendum will lead to violence and civil war.
But East Timor is undoubtedly at a very tense and delicate stage in which the possibility of violence remains high. Indonesia's occupation of the country, following a brutal invasion in 1975, led to the deaths of an estimated 200,000 people; on the pro-independence side, there is an assumption that, in a fair vote, they would win an overwhelming victory. In order to avoid further violence, the CNRT has announced that it will hold no more rallies. And, despite the depredations of the militias, who drove tens of thousands of people out of their homes, some 460,000 of East Timor's 800,000 population have registered for the referendum, a figure that far exceeds the most optimistic expectations.
Two questions remain: can the small UN force hold the Indonesian police to their promise, so far consistently broken, to stifle intimidation during the campaign and on the voting day? And will a vote for independence provoke a violent reaction among the supporters of autonomy within Indonesia?Reuse content