A state-appointed human rights court acquitted the former commander of Indonesian troops in East Timor of crimes against humanity in the territory in 1999, prompting protests by rights groups.
The "dignity and position of Brigadier General Tono Suratman should be restored to him" following the verdict, said Chief Judge Andi Samsan Nganro.
Suratman was the 11th member of the police or military to be acquitted over the savage military-backed militia violence against East Timorese independence supporters.
Suratman, a member of the Kopassus special forces, thanked the judges for "a fair trial." He encouraged soldiers, including those now mounting an assault against separatist rebels in Aceh province, never to hesitate in performing their duties.
Human rights groups have derided the court, which was set up to deflect pressure for an internationl tribunal into the bloodshed, as a sham.
Suratman was accused of having failed to prevent or control violence at a refugee-packed church in Liquica on April 6, 1999 and at a refugee-packed residence in Dili on April 17 that year. A total of 20 people were killed at Liquica while 12 died in the attack on the residence of pro-independence leader Manuel Carrascalao in Dili.
Judge Nganro said prosecutors had not proved that any members of the armed forces who were under Suratman's command were involved in the massacres. He said that victims who testified in court had contradicted each other over the identity of the soldiers they said had taken part.
The court has now acquitted 11 security force members and one civilian. Five people – two army officers, a former Dili police chief, the former civilian governor and an ex-militia chief – have been ordered jailed. All are free pending appeals. One general is still awaiting a verdict.
Munarman, who heads the Indonesia Legal Aid foundation, said the verdict was "not surprising." "The construction of the ad hoc rights court is clearly aimed at trapping the perpetrators at the scene, not those who gave the command," he said. Human rights activist Munir also said he was not surprised by the verdict on Suratman.
"The human rights trials, from the beginning, have only been the government's means to declare that high-ranking officials are immune from the law," he told AFP.
"Sure, they are being put on trial but they know from the beginning that in the end they will walk free and the civil servants and the East Timorese militia will be sacrificed."
Pro-Jakarta local militiamen organised by the Indonesian army waged a campaign of intimidation before East Timorese voted in August 1999 for independence, and a scorched-earth revenge campaign afterwards. At least 1,000 people are estimated to have died and whole towns were burnt to the ground.
Prosecutors in East Timor have separately indicted Suratman and numerous other Indonesian officers for crimes against humanity, but Jakarta refuses to hand any of them over.