CAMBODIA'S UN-backed Khmer Rouge tribunal has charged one of the murderous regime's commanders with crimes against humanity that includes the torture and murder of two Australian yachtsmen.

The move to charge Meas Muth, the former Khmer Rouge navy chief, defies Cambodia's strongman prime minister Hun Sen who opposes the partly Australian funded tribunal pursuing any more prosecutions.

Mr Hun Sen warned in a speech last week that if the tribunal targeted more defendants it could incite former Khmer Rouge members to start a civil war.

Meas Muth, in his 70s, was navy chief when his men captured Australians Ronald Keith Dean and David Lloyd Scott after their yacht had strayed into Cambodian waters at a time in the early 1970s when the world was unaware of a reign of terror under fanatical Khmer Rouge leader Pol Pot.

Dean, a 35-year-old Sydney hotel and club worker and Scott, believed to be about the same age from Western Australia, suffered extreme torture at Cambodia's notorious Tuol Sleng interrogation centre, 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 told the tribunal that one Western man held at Tuol Sleng, possibly one of the Australians, was taken by guards to the road outside the centre, had a tyre placed over him and was set alight and burned alive.

Meas Muth, who rose to the rank of general in Cambodia's military after defecting from the Khmer Rouge, was for years believed to be a high-level adviser to Mr Hun Sen's Defence Ministry.

Some of the accusations against Meas Muth relate the torture and killing of Vietnamese, Thais and other foreigners captured at sea or on disputed island territory during the Khmer Rouge's rule of Cambodia when an estimated 1.7 million died from starvation, execution or disease.

The tribunal has also announced charges against Im Chaem, a Khmer Rouge district commander who headed a security centre in the country's north-west where an estimated 40,000 people died.

But the laying of them has escalated tensions with Mr Hun Sen, a ruthless former Khmer Rouge cadre who throughout three decades of rule has often dealt ruthlessly against those who oppose him.

Neither Meas Muth nor Im Chaem could be reached for comment.

Mr Hun Sen has issued a number of warnings about the tribunal pursuing more than five of the Khmer Rouge's top officials.

"The value of peace and the cost of human lives have to be considered," he said last week.

Some tribunal observers believe Mr Hun Sen will move to block the prosecutions against Meas Muth and Im Chaem going ahead.

The charges must be accepted by the court's senior judges before the two are indicted to face trial.

Tribunal spokesman Lars Olsen said the two were charged in absentia to expedite the legal process by not seeking arrest warrants beforehand.

"Decisions on whether these cases will end up with indictments or dismissals are expected next year, and the charged persons are presumed innocent until proven guilty through a final judgement," he said.

The tribunal that has cost more than $150 million has been dogged by walkouts, strikes and allegations of political interference by Cambodia's government.