The ballot saw East Timorese vote overwhelmingly in favour of separating from Indonesia, which invaded the former Portuguese colony in 1975.
Gross rights violations
The commission's report says "gross human rights violations" took place, pointing the finger at pro-Indonesian militia groups, Indonesia's military, its civilian government and police.
The CTF will officially present its findings to the presidents of Indonesia and East Timor at a meeting in Bali on Tuesday.
If approved, the report would be the first time the Indonesian government has acknowledged the role it and its security forces played in the violence.
|East Timor's troubled history
East Timor was a Portuguese colony from the mid 1500's, until it declared independence in November 1975.
Just nine days later, Indonesia invaded and occupied the island. Up to 250,000 East Timorese died over 24 years of occupation.
August 1999 saw East Timorese overwhelmingly vote for independence, in a UN-supervised referendum.
The vote triggered a scorched-earth campaign of violence by departing Indonesian forces and Jakarta-backed militias, killing up to 1,500 and forcing hundreds of thousands to flee.
An Australian-led intervention force helped restore order and in May 2002 East Timor was declared an independent state.
The 300-plus page report catalogues a list of abuses committed including murder, rape and other forms sexual violence, torture, illegal detention, forcible transfer and deportation.
It said civilian officials provided funding and weapons to pro-Indonesian militias in order to intimidate, threaten and force people to vote for integration with Indonesia.
"Viewed as a whole, the gross human rights violations committed against pro-independence supporters in East Timor in 1999 constitute an organised campaign of violence," the report's authors say in their conclusion.
"The commission recommends that the two presidents together acknowledge responsibility for past violence and apologise to the people of the two nations and especially to the victims of violence for the suffering they have endured."
The report also pointedly recommends that there be no amnesty given to the perpetrators of the violence.
"The commission concludes that amnesty would not be in accordance with its goals of restoring human dignity... Therefore, the commission does not make any recommendations for amnesty," it said.
Al Jazeera's Marga Ortigas, reporting from East Timor, said many in East Timor had expected a whitewash, but the report uses much stronger language than had been anticipated.
She said the report was a clear acknowledgement that abuses occurred, but questions remain over what will happen next.
The commission itself has no power to prosecute individuals and there is speculation the Indonesian and East Timorese presidents will accept the report but not follow up with any prosecutions for the sake of maintaining friendly relations.
East Timor was formally declared independent in 2002, but in the subsequent six years it has been wracked by political instability and remains one of the poorest countries in Asia.
Earlier this year the country's president and prime minister both survived an assassination attempt.
Given its internal problems and its tiny size compared to Indonesia, East Timor's leaders have generally been wary of raising the issue of the 1999 bloodshed for fear of upsetting Jakarta.
Nonetheless human rights groups have said they will continue to push for the trial of alleged leaders of the violence, including the former head of the Indonesian armed forces, General Wiranto.
Wiranto, who was in charge of security at the time of the independence vote, has denied any wrongdoing.