Cambodian police and officials had for months refused to issue a warrant for the arrest of Meas Muth on genocide and other charges as the country's strongman prime minister Hun Sen opposed any expansion of prosecutions at the partly Australian-funded tribunal.
Meas Muth, now in his 70s, was chief of the Khmer Rouge navy when his men captured Ronald Keith Dean and David Lloyd Scott after their yacht had strayed into Cambodian waters at a time the world was still unaware of a reign of terror under fanatical Khmer Rouge leader Pol Pot.
Mr Dean, a 35-year-old Sydney hotel and club worker, and Mr Scott, believed to be about the same age from West Australia, suffered extreme torture at Tuol Sleng, possibly for months.
Both men signed false confessions saying they were CIA agents in an apparent attempt to avoid their executions.
A guard at Tuol Sleng has told the tribunal that one of the Westerners, possibly one of the Australians, was burned alive on a road outside the centre.
Three guards took him outside the centre, sat him down on the road, placed a tyre over him and set him alight, said Cheam Soeu, who worked as a guard at the centre for two years.
The trials, officially called the Extraordinary Chambers in the Courts of Cambodia, have been racked by bitter internal disagreements, staff resignations and cost blow-outs.
Cambodian police and officials have not cooperated in prosecuting new suspects pursued by the tribunal's international judges.
Only three Khmer Rouge cadres have been found guilty by the tribunal that was established in 1997.
Mr Meas Muth rose to the rank of general in Cambodia's military after defecting from the Khmer Rouge, becoming a high-level adviser to Mr Hun Sen's Defence Ministry.
UN and other investigators have found that Mr Meas Muth participated in a plot to purge the Khmer Rouge of ''undesirable elements'' that resulted in thousands and quite possibly tens of thousands of deaths.
He has been charged with genocide and crimes against humanity including murder, extermination, enslavement, imprisonment, torture, persecution and other inhumane acts.
Mr Meas Muth told Cambodian journalists in 2011 that he was not one of the Khmer Rouge leaders most responsible for what happened during the organisation's rule and therefore should not be put on trial.
He has not commented publicly on the formal laying of charges against him.