The Special Air Services (SAS) member, whose identity has not been made public, was seen shooting the Afghan man in 2012 in video filmed by another soldier and broadcast Monday by national broadcaster ABC.

The Defence Department, which is carrying out a wide-ranging probe into alleged war crimes by Australian forces in Afghanistan, issued a statement late Thursday calling the ABC story "serious and disturbing".

It said the soldier in the footage was identified Thursday and immediately suspended from duty.

Defence Minister Linda Reynolds issued a separate statement saying she had referred the "alleged serious criminal conduct" of the soldier to the Australian Federal Police.

The ABC report said the SAS unit was helicoptered into an Afghan village in search of a suspected bomb-maker.

Video taken by a helmet-mounted camera carried by the unit's dog handler, showed a soldier identified only as "Soldier C" running through fields of tall grass and coming upon a man who had been brought to the ground by a military dog.

The Afghan appeared to be holding a string of prayer beads but no weapons. Soldier C is seen shooting him three times from about two metres (yards) away.

The ABC report came as Australian authorities were already investigating more than 50 alleged war crimes by SAS troops, including the killing of civilians and prisoners.

A report issued last month by the Inspector-General of the Australian Defence Force said 55 separate incidents were being investigated as part of a years-long probe into war crimes allegations against Australian soldiers serving in Afghanistan.

The probe was launched in 2016 in response to what the watchdog called "rumours" of "very serious wrongdoing" over more than a decade by Australian special forces in Afghanistan.

Elite Australian commandos were deployed alongside US and allied forces in Afghanistan following the September 11, 2001 attacks. NATO and its allies pulled combat forces from the country in 2014.

The ongoing inquiry, led by judge Paul Brereton, has called 338 witnesses and is now "approaching the final stages of evidence-taking".

At least five investigations into alleged abuses by Australian special forces in Afghanistan are currently under way.