Investigators probing allegations of war crimes by Australian special forces soldiers have travelled to Afghanistan and interviewed witnesses.

Key points: Investigators have travelled to Afghanistan as part of an inquiry into "allegations and rumours of misconduct" by Australian special forces

Investigators have travelled to Afghanistan as part of an inquiry into "allegations and rumours of misconduct" by Australian special forces They conducted interviews with witnesses in Afghanistan

They conducted interviews with witnesses in Afghanistan The inquiry relates in part to incidents described in the ABC's "The Afghan Files" reporting

The ABC understands NSW Supreme Court Justice Paul Brereton and other staff representing the Inspector-General of the Australian Defence Force (IGADF) were in Kabul recently interviewing witnesses as part of their investigations.

Justice Brereton, who is also a Major-General in the Army Reserve, heads an IGADF inquiry into "allegations and rumours of misconduct" by Australian special forces during the 18-year-long war in Afghanistan.

The inquiry began in early 2016 after the rumours of alleged war crimes that had swirled within the special forces community and the wider Australian Defence Force could no longer be ignored.

A spokesperson for Defence said it would not be appropriate to comment as the inquiry was ongoing.

The fact Justice Brereton and his staff have travelled to Afghanistan, despite the significant logistical and security constraints involved in visiting the country, is hugely significant.

The length of time the inquiry has taken so far and the secrecy surrounding it have led some commentators and Defence insiders to question its effectiveness and the impact it is having on the morale of Australia's special forces units.

Justice Brereton's willingness to interview Afghans about the allegations against Australian troops shows the inquiry will not only be reliant on official Defence Force reporting and evidence given by Australian personnel.

The ABC has previously reported on a number of incidents involving Australian special forces troops from the Special Air Service and 2nd Commando Regiment that the IGADF inquiry is investigating.

Among them was an alleged incident in a small village in Uruzgan province called Darwan, in which three men were killed by Australian SAS troopers searching for a rogue Afghan soldier who murdered three Australian soldiers at a patrol base.

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Villagers from Darwan told an Afghan journalist retained by the ABC that one of the dead men, Ali Jan Faqir, was either kicked or thrown from a high wall into a ditch while handcuffed and then shot, or shot first then thrown from the wall.

The villagers claimed the two other men — Yaro Mama Faqir and Haji Nazar Gul — were unarmed and under detention when they were shot dead in a room used to store almonds.

Australian soldiers during an operation in Helmand Province, near Darwan in 2011. ( Supplied: Department of Defence )

The IGADF inquiry is also investigating a number of other incidents in which Afghan men, and in some cases children, were allegedly shot dead by Australian troops.

Among them is the alleged killing of a man named Bismillah Azadi and his young son, Sadiqullah, in the north-west of Uruzgan Province in September 2013.

The Australian special forces claimed that Azadi pointed a pistol at them during a night raid targeting a high-value Taliban target, so they shot him dead, but were unaware the child was hidden under blankets in the room.

However, relatives of the dead man and child told the ABC that Azadi was unarmed when killed and had no links to the Taliban.

The incident was among those referred to in the 'Afghan Files', a series of stories which led to a raid by the Australian Federal Police on the headquarters of the ABC earlier this year.

Another incident reportedly under the microscope is the alleged killing of an Afghan businessman, Hayat Ustad, at his warehouse in the capital of Uruzgan province, Tarin Kot, in April 2011.

Again, the Australian troops who allegedly killed Ustad said he was armed and threatening them when he was gunned down.

However, a friend of Ustad, Mohammad Hassan, who was at the warehouse when he was killed, told a reporter from the ABC's Four Corners in 2011 that when the Australians arrived they asked who the manager of the warehouse was.

Mr Hassan said that when Ustad raised his hand and said "I am," an Australian soldier led him out of sight and then shot him dead. Mr Hassan said Ustad was unarmed and not trying to flee.