(Adds reactions from victim, Indonesian foreign ministry)

By Olivia Rondonuwu

JAKARTA, July 11 (Reuters) - Indonesian security and civilian forces carried out "gross human rights violations" during East Timor's 1999 independence vote, a state-backed probe has found.

The Commission of Truth and Friendship (CTF) is expected to submit its findings to Indonesian President Susilo Bambang Yudhoyono and East Timor President Jose Ramos-Horta for their approval on July 15.

If approved, the over 300-page report would be the first time Jakarta is acknowledging the role of the Indonesian military, police and civil government in the violence.

The report, a copy of which was seen by Reuters, also recommended the two presidents apologise to their people.

East Timorese voted overwhelmingly to split from Indonesian rule in 1999 and the United Nations estimates about 1,000 East Timorese died during the post-vote mayhem.

The two governments set up the CTF in 2005 to look into the violence, but it has no power to prosecute, prompting criticism that it serves to whitewash atrocities. It has been boycotted by the U.N.

The commission concluded "gross human rights violations in the form of crimes against humanity did occur in East Timor in 1999 and that these violations included murder, rape and other forms of sexual violence, torture, illegal detention".

It said pro-autonomy militia groups, Indonesia's military, civilian government and police must bear institutional responsibility for gross human rights violations targeted against civilians perceived as supporting the pro-independence cause.

The commission said civilian officials provided funding and weapons to the militia groups 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," it said.

"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."

NO AMNESTY

The report also said the commission abandoned its right to ask the governments to grant amnesty to the perpetrators.

"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.

Agus Widjojo, a CTF commissioner from Indonesia, said there would be no prosecution of individuals as criminal law did not recognise institutional responsibility.

East Timor leaders have appeared wary of upsetting its giant neighbour over the issue, but rights groups have said they will push for a trial of retired General Wiranto, under universal jurisdiction after the report is submitted.

Wiranto, who was in charge of security at the time of the independence vote, has denied any wrongdoing.

But East Timor victims said they were not satisfied.

"I don't want reparation, the money cannot buy my dignity as a woman. I want them to face justice and stay in jail," Maria Do Rego, a victim of sexual violence in 1999, told Reuters.

"We ask the Indonesian government as an institution and military elements as individuals to apologise for their criminal acts in East Timor."

An Indonesian foreign ministry spokesman said Indonesia would accept the report and study its contents thoroughly.

"As two countries that have given their mandate, of course we have an obligation, moral necessity, to accept the contents of the report," Teuku Faizasyah said.

"Our offspring may not want to be burdened by an issue that has become, say, a pebble in our relationship." Indonesia's former foreign minister Ali Alatas once described East Timor as "a pebble in our shoe".

Indonesia invaded East Timor in 1975, after Portugal abruptly pulled out of a colony it had ruled for three centuries, and annexed the territory later that year, maintaining a heavy and at times brutal military presence. (Editing by Sugita Katyal and Bill Tarrant)

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