Human rights reports leaked to the ABC support allegations that some Australian special forces unlawfully killed an unarmed farmer and his child during a controversial raid in Afghanistan's Uruzgan province.

In 2017, the ABC's Afghan Files series reported that farmer Bismillah Jan Azadi and his young son Sadiqullah were shot and killed by Special Air Service Regiment (SAS) troopers in September 2013.

The report said they were sleeping in their village of Ala Balogh on the outskirts of the Uruzgan capital Tarin Kot when the Australian raid began.

The SAS troopers were later cleared by a military investigation, after the soldier who shot the pair told the inquiry Bismillah had pointed a pistol at him.

But in an interview with the ABC, Afghanistan's top human rights official has contradicted this, saying her organisation's investigation determined that the man was an unarmed civilian.

ABC raided over Afghan Files

The Afghan Files series is now the subject of a controversial Australian Federal Police (AFP) investigation.

In June, AFP officers raided the ABC's Sydney headquarters and seized documents, acting on a warrant that named reporter Dan Oakes, producer Sam Clark and ABC director of news Gaven Morris.

AFP officers sit with the ABC legal team and an IT specialist while the raids took place. ( ABC News: Brendan Esposito )

Now the ABC has obtained more than 90 files from Afghanistan's Independent Human Rights Commission (AIHRC), one of which is a report into the killing of Bismillah and his son.

The AIHRC is Afghanistan's national human rights agency, established under the country's constitution, which has the power to investigate allegations of human rights abuses.

The files obtained by the ABC cover 2010 to 2013 and include investigation reports, witness testimonies, photographs, detention records and civilian casualty logs.

"Our colleagues visit sites where the reported abuse has happened, they engage with victims, they engage with other eyewitnesses, they engage with authorities, they visit hospitals, so it is a very thorough methodology," said AIHRC chair Shaharzad Akbar.

The files reveal Bismillah's family made a detailed complaint to the commission about the killing, alleging it was completely unwarranted and that the farmer did not own a pistol.

'The child was killed lying in his father's arms'

The AIHRC report of the incident states the target of the joint Australian-Afghan army raid was a Taliban commander called Mula Sardar, who was captured in the night operation.

Esmat Jan was inside a house while his father and brother were shot by Australian soldiers. ( ABC News: Bilal Sarwary )

"During this time, some foreign soldiers climbed onto the roof of Mula Sardar's neighbour's house," the AIHRC file states.

"Some soldiers entered the house, at this point one of the foreign soldiers shot and killed both Bismillah Jan, 35 … and his six-years-old son Sadiqullah while [they were] asleep under a blanket on the veranda."

The file includes testimony from Bismillah's cousin and neighbour Mohammad Masoom, who reported that he found the man and his son "killed under the blanket [which] had bullet holes and they were bleeding out [of] the blanket."

"[The] child was also killed lying in his father's arms. The wounds on his stomach were plastered and needles were left on his chest — probably it was to treat him," Mohammad told AIHRC investigators.

Mohammad says some of the foreign troops then searched the family home.

The ABC tracked down another of Bismillah's sons, Esmat Khan, in Ala Balogh village.

He confirmed in a recorded interview that his father and brother were asleep on the verandah when the Australians and their Afghan allies arrived.

"As soon as they came, they shot them. They didn't ask him anything," Esmat said.

"His body was riddled with shots like a colander … they had shot him in the head, on his sides. They had killed my brother in that manner also, he was shot a lot."

Esmat, who was inside the house while his father and brother were shot, says he was stopped from going to them until after the Australians had searched the family home and left.

"There were boot marks on [my father's] shoulder," he told an Afghan journalist working for the ABC in a recorded interview.

"There were boot marks on his head also."

Esmat backed Mohammad Masoom's witness account, recorded in the Afghan human rights files, that there appeared to have been attempts by the Australians to try to treat his six-year-old brother's wounds.

"They had given him bandages and given him injections … they didn't remove those bandages," he said.

Esmat says when he went to the bodies he found $US1,500 placed with them. He rejected Australian special forces claims that his father was armed.

"He was a farmer. He hadn't seen a gun … he was deep asleep when he was shot dead," he said.

'Our poor father was killed for nothing'

The SAS soldiers involved in the raid were part of Defence Force's Special Operations Task Group that was on its 20th rotation through the province.

Shaharzad Akbar is chair of the Afghanistan Independent Human Rights Commission. ( ABC News: Andrew Quilty )

Bismillah's son Esmat told the ABC he later met with a member of the Australian military who was not present at the raid to discuss his father's killing.

"They said: 'We were mistaken, forgive us.'

"We said: 'How can we forgive you? Why didn't you think about this earlier on?'

"We didn't forgive them."

Esmat said the Taliban commander who was captured in the raid, Mula Sardar, was not held by the Australians for very long.

"[Mula Sardar] was jailed for six to seven months and they (the Australians) freed him again," Esmat said.

"He is free nowadays. Our poor father was killed for nothing."

Mula Sardar's capture has been confirmed to the ABC by village elder Haji Toor Jan, who says Sardar was imprisoned for about six months and freed after tribal elders lobbied for his release.

The ABC interviewed the head of the AIHRC, Shaharzad Akbar, about the case and commission's investigation.

"Our investigation states that this man [Bismillah], was not in any way attacking the Australian forces,'' she said.

"He was not a threat. He was a civilian. So, we haven't had any proof to show that he was in any way engaged in combat."

Amir Muhammed Akhundzada said the villagers laid out the bodies at the Uruzgan governor's house. ( ABC News: Bilal Sarwary )

Akbar said she welcomed any further investigation into the alleged wrongful killing of civilians in the hope that "justice is delivered to the victims".

One who saw firsthand the tragic aftermath of the raids was the then-Uruzgan governor Amir Muhammed Akhundzada, who said he made an official complaint to the Australians about the deadly raid.

"Some of the [Australian] operations were positive, but some operations had shortcomings and we had many quarrels with them," the former governor told the ABC's reporter in an interview in Kabul.

"[The villagers] brought the bodies [from the Ala Balogh raid] to the governor's house. There were too many people, they were sobbing.

"I called the commander responsible for the raids. I told him about our painful situation and I made an official complaint from the governor's office."

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Defence reports 'could cause damage': FOI rejected

The ABC can confirm the Ala Balogh raid is being investigated by the Inspector-General of the Australian Defence Force as part of the long-running probe into possible unlawful killings by Australian troops in Afghanistan.

The inquiry, which has been underway since May 2016, was initiated after rumours of alleged war crimes circulated through the special forces community and were backed up by research into special forces operators undertaken by Canberra-based sociologist Dr Samantha Crompvoets.

Assistant Inspector General of the Australian Defence Force Justice Paul Brereton was appointed to head the inquiry.

Dozens of former and serving soldiers have been interviewed and earlier this year Justice Brereton travelled to Afghanistan to conduct further inquiries in Kabul.

In July, the ABC lodged a freedom of information request, seeking Defence Force investigation reports about the Ala Balogh operation and another Australian raid from the year before which had also led to civilian deaths.

The request captured 200 pages of material, but the Defence Force has refused to release a single page.

In its rejection notice it said any release could "cause damage to the security, defence or international relations of the Commonwealth" and that the material comprises information on "the tactics, techniques and procedures" used by Defence during warlike operations.

But most telling of all, the request was rejected because of the Inspector General's inquiry, and the release of the material could "jeopardise the outcome of the investigation".

When the ABC put questions to the Defence Department about the Ala Balogh raid, a spokesman said it was not appropriate for Defence to make any further comment at present in order "to protect the integrity and independence of the inquiry and the reputations of individuals who might otherwise be unfairly affected."

The refusal to release details about Defence Force investigations into such operations is not new.

Defence previously released redacted investigations reports into civilian casualty incidents but following one report released in 2014 relating to a 2012 incident, no other Afghanistan inquiry reports have been made public since then.

Additional reporting by Bilal Sarwary