More than 1,000 people were killed and injured in violence around the poll
East Timorese victims of the violence of 1999 and of Indonesia's occupation have yet to receive any justice, says a report by Amnesty International.
Many perpetrators of war crimes and crimes against humanity between 1975 and 1999 have still not been brought to trial, the human rights group says.
Amnesty says East Timor is haunted by a "culture of impunity" - a decade after voting for independence from Indonesia.
The group has called on the UN to set up an international criminal tribunal.
Donna Guest, Amnesty International's Asia-Pacific deputy director, said the victims of the atrocities need a "clear commitment" from both the Indonesian and Timorese governments as well as the UN to investigate all allegations and bring those responsible to trial.
"Disappointed Timorese victims provided testimonies time and time again to various mechanisms, but they have still not seen significant signs of accountability," she said.
The Timorese and Indonesian governments have "chosen to avoid justice for the victims", which has "weakened the rule of law in both countries", she went on to say.
Ten years ago an overwhelming majority of East Timorese people voted for independence from Indonesia.
But in the lead-up to the vote and in its aftermath, militia loyal to the Indonesians went on a rampage.
Most people in East Timor live on less than $1 a day
Amnesty International says at least 1,200 people were killed, and the crimes included rape, disappearances, arbitrary arrests and unlawful killings.
Suai was the location of one of a number of deadly church massacres in 1999.
At least 26 people were killed in the Ave Maria church, and locals say hundreds more remain unaccounted for, the BBC's Karishma Vaswani reports from Suai.
Many of the victims of the violence are angry and disappointed with their government for not punishing those responsible for the crimes, she adds.
An ad hoc Human Rights Court set up by Indonesia and the UN Special Panels in East Timor tried 18 people for alleged crimes committed during 1999 but all were acquitted, the Amnesty report says.
Only one person convicted by the UN Special Panels is still serving a prison sentence, it adds.
A joint Indonesia-East Timor Truth and Friendship Commission was held in 2005, but it did not have the power to prosecute.
East Timor has opted for a conciliatory approach with Indonesia since gaining independence in 2002.
The government has said that continuing to focus on the past will not allow the nation to move forward, and that its priorities are to develop the local economy so the country's people can begin to rely on themselves instead of foreign aid.
But that is a monumental task, our correspondent says.
East Timor remains one of the poorest countries in Asia. Most people live on less than $1 a day.
Ten years on from the historic independence vote, the optimism among East Timor's people is still evident, she adds.
But Amnesty has warned that the country's leaders must deliver on the promises they have made to their citizens, before it is too late.