An investigation into allegations of unlawful killing and brutality by Australian special forces in East Timor led to a soldier being charged with kicking a militiaman's corpse after an ambush, Army chief General Peter Leahy said.

Leahy said another soldier was counselled over gender and workplace harrassment after the investigation, which was carried out by the Australian Defence Force with assistance from Federal Police and the United Nations.

Leahy said 19 allegations of misconduct and mistreatment against Australian soldiers carrying out peace-keeping operations following East Timor's independence referendum in 1999 were investigated. Thirteen were found to be unsubstantiated and though elements of complaints were upheld, investigators found no offence was committed.

The investigation centred on a gun battle on October 6, 1999 near Suai on East Timor's border with West Timor, in which two militiamen were killed, nine wounded and more than 100 captured. Two SAS troops were also wounded in the firefight.

Rumours of subsequent misconduct circulated in defence circles, including claims that a senior special forces soldier, angred over his soldiers' injuries, shot dead one or more of the captives.

Investigators exhumed the bodies of the two dead militia men from a cemetery in Dili late last year but found no evidence of battlefield executions and concluded the deaths resulted from "professionally conducted counter-ambush measures".

The militiamen belonged to the pro-Jakarta Laksaur group responsible for some of the worst atrocities in the violence that followed an overwhelming vote for independence by the East Timorese in August 1999.

Most of the militia escaped to West Timor and Indonesia – never to be brought to justice for the hundreds of murders, torture, arson and destruction for which they were blamed.

Leahy said the unidentified Special Air Services soldier charged with kicking the corpse would face an open trial at a date yet to be set.