Mr Suratman is the 11th defendant to be acquitted over East Timor
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The former commander of Indonesian troops in East Timor has been acquitted of crimes against humanity by a court in Jakarta.
Chief Judge Andi Samsan Nganro said the "dignity and position of Brigadier General Tono Suratman should be restored to him" as a result of the verdict.
Prosecutors had demanded a 10-year jail term for Mr Suratman, who controlled Indonesian troops in East Timor up to two weeks before the province voted overwhelmingly in favour of independence, in August 1999.
The trial is just a show. It is meant to preserve
impunity, to protect the generals, while in reality sacrificing
the people down below
Hendardi, Indonesian Legal Aid and Human Rights Association
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After the hearing, Mr Suratman thanked the judges for "a fair trial", and encouraged other Indonesian soldiers to perform their duties without hesitation - including those now involved in an assault against separatist rebels in the province of Aceh, the French news agency AFP reported.
The United Nations estimates more than 1,000 people were
killed in the violence that erupted in 1999, after the Jakarta government finally agreed to allow the East Timorese to vote on their independence, following a 25-year separatist struggle.
Mr Suratman is the 11th member of the Indonesian security forces to be acquitted over attacks against pro-independence supporters in East Timor.
Five others have been found guilty, although all are still free pending appeals.
There is one more general awaiting a verdict, Major-General Adam Damiri.
He is the highest ranking suspect and is accused of having failed to prevent his troops from committing atrocities in East Timor, but he has so far failed to appear before the court.
Lawyers for General Damiri said he was prevented from appearing for the third time on Thursday because he was busy directing military operations against separatist rebels in the province of Aceh.
Church massacre
Brigadier Suratman was accused of failing to prevent two massacres in April 1999, in which a total of 32 people were killed.
Twenty people died during violence in a packed church on 6 April, while another 12 died less than two weeks later, during an attack on the home of the pro-independence leader Manuel Carrascalao.
Judge Nganro said the prosecution had been unable to prove that any of Mr Suratman's troops were involved in the massacres.
But human rights activists have criticised the Jakarta court for failing to punish those responsible for atrocities in East Timor.
The Indonesian Legal Aid and Human Rights Association told
Reuters news agency that Mr Suratman's trial was "just a show" meant to "protect the generals, while in reality sacrificing
the people down below".
The result will "make those who rule in Aceh become more powerful and arrogant", said Hendardi, the organisation's head.
Indonesia is in the fourth day of a crackdown against separatist rebels in Aceh, after a five-month-old peace agreement fell through on Monday.
Acehnese rebels, like those in East Timor, are fighting for independence from Jakarta.
But analysts say Aceh has a weaker legal basis for its independence claim.
Aceh was made part of Indonesia when the Dutch colonialists left in 1945. But East Timor was never part of the initial Indonesian archipelago, being independent at the time the Jakarta army invaded in 1975.