Video footage of an Australian soldier shooting dead an apparently unarmed Afghan man has the potential to result in charges of war crimes.

A “deeply disturbed” Defence Minister Linda Reynolds reiterated the need for an inquiry into allegations against special forces after a Four Corners investigation uncovered helmet camera video of a Special Air Service operator shooting an Afghan man three times in the head.

The seemingly defenceless man in his 20s could be seen cowering on the ground of a wheat field as the SAS operator aims an assault rifle at him and fires off the three shots on a May 2012 day.

The alleged incident, which was one of a number of allegations uncovered by Four Corners, occurred just three minutes after their helicopter swooped down near the village of Deh Jawz-e Hasanzai.

Before the soldier started shooting, he could be heard twice asking a nearby patrol commander “You want me to drop this c***?”

An Australian Defence Force (ADF) investigation later ruled the soldier acted out of self-defence and deemed the killing as justified.

According to the ABC, the soldier is still a member of the special forces.

WARNING: Graphic footage

A former SAS soldier has also told the program he saw a further three incidents of alleged murder.

Afghan villagers provided details, saying a SAS squadron raided the village of Sola in Uruzgan province on August 31, 2012, days after a rogue Afghan soldier killed three Australian troops.

Villages were allegedly blindfolded and tied up, and a local imam and his son were shot dead.

Defence Minister Ms Reynolds is calling on the Inspector-General of the Australian Defence Force to investigate allegations against special forces in Afghanistan from 2005 to 2016.

The military watchdog is investigating 55 separate allegations of unlawful conduct in Afghanistan by Australian soldiers.

“Where serious allegations are raised, Australians would rightly expect they are thoroughly examined,” she said.

“The Chief of the Defence Force has advised me that the IGADF will soon provide a report on the findings of the Afghanistan Inquiry.”

Amnesty International Australia’s Tim O’Connor backed calls for a federal inquiry, saying international law emphasises the need for soldiers to avoid civilian casualties and use proportionate force, but not when there is a high risk of non-combat deaths.

“People have a right to know if the government they elected and the departments and services they pay for are behaving legally and ethically,” Mr O’Connor said.

“The ADF Inspector-General must fully investigate the claims made in the program and it is critical that the Australian Defence Force is transparent about its involvement, and informs the Australian media and public as soon as possible.”

In a statement to the ABC, the ADF Inspector-General said it was investigating “whether there is any substance to rumour and allegations” about possible war crimes committed by Australian special forces in Afghanistan.

-with AAP