Defence Minister Linda Reynolds says she is "deeply disturbed" after new allegations emerged that Australian special forces soldiers killed unarmed Afghans.

ABC Four Corners has aired footage from a helmet camera showing an Australian soldier shooting dead an unarmed Afghan in a wheat field in May 2012.

Former SAS soldier Braden Chapman also told the program he saw three incidents of alleged murder during his deployment to the war-torn country.

Australian Department of Defence

The footage shows an Australian soldier aiming his rifle at the Afghan man lying on the ground, who appears to have prayer beads in his hand.

The soldier calls out to his superior officer three times, saying: “Do you want me to drop this c---?”

He then shoots the young man three times from about two metres away.

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"I am deeply disturbed by what has been aired in tonight's Four Corners report," Senator Reynolds said in a statement late on Monday.

She said she had steadfastly supported an inquiry by the Inspector-General of the Australian Defence Force (IGADF) into allegations against special forces in Afghanistan from 2005 to 2016.

AAP

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."

An ADF investigation ruled the killing shown in the video was justified because it was in self-defence.

The soldier depicted, who still serves in the special forces, said he shot Afghan Dad Mohammad because he had seen him with a radio.

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The soldier also claimed he fired from 15 to 20 metres away – but this evidence contradicts his proximity with the victim as shown on the video.

ADF investigators found the Afghan was lawfully killed as he posed a direct threat to Australian soldiers.

The killing was one of a series of cases aired by Four Corners that may constitute war crimes.

This included the alleged murder of another Afghan man Haji Sadr, who was allegedly beaten to death after being treated by an Australian medic.

The medic had treated the Afghan man for a gunshot wound to the leg, before he was allegedly taken away by another special forces soldier.

This soldier later reported him dead, allegedly describing how he did not make it.

Afghan villagers also said an SAS squadron raided the village of Sola in Uruzgan province on 31 August, 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.

Human Rights activist Shahrzad Akbar said the men were unarmed and civilians.

But an Australian defence investigation found both deaths were justified.

Former SAS soldier Braden Chapman told the ABC soldiers had joked about “the size of the rug that they’ve swept everything under”.

“One day everything’s going to come out and people were going to go to jail for murder,” he recounted them saying.

He said one Special Forces soldier had told him to be “prepared for this deployment” because he would have to be “OK” with him “putting a gun at someone’s head and pulling the trigger”.