The last image Hazratullah has of his father Haji Sardar Khan is truly nightmarish.

It is of Sardar, bag over his head, bleeding profusely from a gunshot wound to the leg, being carried off like a sack over the shoulder of an Australian soldier.

Minutes earlier, the young Hazratullah said he watched his father venture unarmed outside their simple mudbrick home to see why soldiers had landed helicopters on the stony plain above their village.

Without warning, he said, the troops fired on his unarmed father, hitting Sardar in the thigh and dropping him to the ground. There he sat bleeding but alive, talking and lucid.

It was then that the Australian troopers pulled a bag over Sardar's head and a soldier hoisted him onto his back and carried him away to a nearby mosque, said Hazratullah.

Haji Sardar Khan's family filmed his dead body, after he was killed during an Australian special forces raid in Afghanistan. ( Supplied )

Prevented by the Australians from going to his father, he heard the old man calling out. Then there was silence.

"We were not allowed inside but we heard shouts and cries for an hour, or 30 minutes," he said.

"When they left the mosque we got inside and they had martyred him. He had bruises all over his neck. Before that he was wounded, but not critically."

Hazratullah's father Haji Sardar Khan, was killed during a raid on his village. ( ABC News: Bilal Sarwary )

Sardar was not the only villager to die that day in mid-March 2012, when the Australians mounted a raid to find a suspected Taliban bomb maker at Sarkhume, a tiny farming community in southern Afghanistan.

In a nearby field, mill worker Mirza Khan was confronted by Australian military dogs clad in special harnesses, villagers say.

As Mirza struggled to push away one of the dogs, the Australians, without warning, fired a volley of shots into his body, according to Hazratullah, who is now in his late teens.

"He was martyred (killed) on the spot … [the Australians] did not get closer to him; they did tell him not to touch the dogs."

The raid might have occurred seven years ago, but residents still vividly recall the mission, that claimed the lives of two civilians and left others injured, as an example of pointless violence.

After the raid they complained to local authorities but the Australians conducted their own internal investigation, which reportedly classified the two dead men as combatants. It also found the raid was justified.

However, like some other controversial Australian special forces operations that provoked such complaints in Afghanistan, the report and the extent of its inquiries have been kept secret.

Now an investigation by the ABC, using reports from Afghanistan's Independent Human Rights Commission (AIHRC), has uncovered concerning allegations regarding the secret operation.

The reports raise questions about the killings, with the head of the commission Shaharzad Akbar telling the ABC that the AIHRC stands by its findings that all the dead and injured were unarmed civilians.

The reports obtained by the ABC were compiled by the AIHRC's staff in Uruzgan province between 2010 and 2013 and recorded numerous alleged human rights breaches by all parties, including some Taliban and Australian soldiers.

The files include investigation reports, witness testimony, photographs, detention records and civilian casualty logs.

"We have reported on any case of civilian casualties that our investigation proved to be true, including the case of Australian forces," said AIHRC chair Shaharzad Akbar.

"It is then the decision of the court to further investigate and determine if these were war crimes."

Earlier, the ABC revealed how one of the reports had reaffirmed allegations first raised in the public broadcaster's controversial 2017 Afghan Files reports about another Australian special forces operation that led to civilian killings at Ala Balogh village in Uruzgan.

Among the reports are accounts of the Sarkhume operation directly contradicting the Australian military's official account of the killings.

'They have slaughtered people standing'

By tracking down villagers and sources associated with the initial complaint, the ABC has confirmed many of the details reported by the AIHRC.

"We don't know, by God, why they were killed," said Abdul Latif — Sardar's eldest son — when he was interviewed about the case by an Afghan journalist working for the ABC.

"Our civilians were killed; they killed our elders ... wherever they have conducted raids, they have slaughtered people standing."

At the time of the raid, Uruzgan was the operational area for Australia's Special Operations Task Group (SOTG) — a combined force of about 320 elite soldiers made up of troopers from the Special Air Service Regiment (SASR) and commandos.

Their mission, which often involved working with Afghan internal security forces known as the Wakunish, was dangerous and conflicted; Australians straddled a line between hunting down high-value Taliban targets while trying to ensure Afghans could go about their lives peacefully.

Operations were nerve-wracking affairs — sometimes involving night raids and room-to-room firefights — in the mudbrick qualas where their battle-hardened Taliban targets hid, and innocent men, women and children slept.

'Boot marks over his heart'

The Sarkhume raid took place in the morning while the villagers were already up and moving about.

According to the AIHRC report into the incident, Sardar had earlier been doing some work repairing a doorway in his home.

A memorial tribute for Haji Sardar Khan. ( Supplied )

He heard the helicopters and had been on his way to see what the Australians were doing but first he took the local shortcut over a broken-down wall to wash some mud from his feet in a drain near his house. It was at this point he was shot.

"Foreigners (Australians) arrived at this moment and shot him in his thigh. He was wounded," said the report.

Haji Sardar left behind a wife, three daughters, four sons and five grandchildren, notes the report.

Hazratullah confirmed the AIHRC account. He was there when his father went outside.

He says the only thing in his father's possession at the time was the old man's treasured transistor radio that he listened to while working in the fields.

"[The helicopters] landed close to our home. My father and I started moving. I stayed there. I was looking after the goats and sheep, they scattered them,'' Hazratullah said.

He told the ABC his father moved to climb the wall into the garden and was shot in the thigh by one of the Australians.

"As soon as they got down (from the helicopter) they started shooting him," said Hazratullah.

He said the Australians did "not issue any warnings — nothing".

"My father was walking by himself, but he fell by the tower and he sat there. [The Australians] came and took him to the side of the house ... he couldn't walk on foot. Blood was dripping from his legs. He would get faint, so they placed him on their back and took him inside the mosque."

The Australians refused to let him or anyone else go to his father, said Hazratullah.

"When he got wounded by the gate they pulled a bag over his head. They wouldn't let one person know the situation of another," he said.

"They had tough rules. Even if you simply looked they would beat you over the head with a gun. They would start kicking you. No-one could look at each other or talk."

A shocking sight greeted Hazratullah and the other villagers when they finally got to examine Sardar's body in the mosque.

"Big fat boot marks were over his heart" when they found the body, Hazratullah said.

"He had bruises on his neck. He was martyred (dead). Before [he was taken inside the mosque] he was wounded, but not critically."

A short time later in the fields, down in the green zone below Haji Sardar's home, the second villager was killed, according to the AIHRC file.

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Another unarmed man killed, say relatives

The AIHRC report said Mirza Khan, aged about 20, had just left his work at the local flour mill and gone into the fields when he encountered a dog belonging to the soldiers.

SOTG soldiers had trained working dogs who would join them on missions. ( Supplied: Department of Defence )

The dog was thought to be one of the SASR's combat assault canines specially trained to apprehend suspected insurgents and warn of enemy positions.

Hazratullah said he saw the attack from a distance. He said the dogs came at Mirza, who tried to keep them away and hit one with "a stone".

"They [the dogs] tore all his clothes. He was moving away from their dogs — they fired a round of bullets and martyred him."

Mirza's corpse had multiple wounds, according to Hazratullah.

"He was covered in blood. A person couldn't look at him. We didn't remove his clothes. We buried him in his clothes," he said.

Mirza's brother, Shaista Khan, did not witness his killing. But when Shaista saw his brother's body before burial, he recalls Mirza was "shot in his lower abdomen, shot in the leg, from this side, shot in the chest".

The relatives of the dead men denied any of them had been armed or were behaving aggressively towards the soldiers.

Mirza Khan was killed during a raid in Sarkhume, Uruzgan Province, Afghanistan. ( Afghanistan Independent Human Rights Commission / translation by the ABC )

Abdul Latif said his father was not armed and did not even own a weapon.

"[The Australians] might be making a justification for themselves," said Abdul Latif.

"Haji Sahib and Mirza Khan didn't have a hand grenade. Haji Sahib didn't know how to use a hand grenade. He didn't even have a knife."

Shaista also denied his brother Mirza posed any threat or carried any weapons.

Abdul Latif's father, Haji Sardar Khan, was killed during a raid by Australian forces in the village of Sarkhume, Afghanistan. ( ABC News: Bilal Sarwary )

His brother had gone to tell two friends to come and drink tea with him while the mill was running to grind the wheat, Shaista said.

"He didn't have anything … [His friends] were at the end of the farm. He told them come and have tea and then he ran back to the mill. The mill was on, flour was processing," said Shaista.

Shaista said he was told that his brother encountered an Australian dog on his way back to the mill and after confronting the animal aggressively, he was attacked.

"It was a yellow Australian dog. [Mirza] was suffering. He had the dog held by one hand and he was shot and when the Australians came over, they shot him even more and made him not function. He let the dog go free."

The villagers said others were roughed up during the raid including a shepherd boy who was hit with a knife handle in the neck after he tried to go to his father.

The AIHRC report into the incident said the boy, named Zabihullah, was four years old.

"[The child] was bashed with a knife on his back by foreigners because he was with his father and did not want to separate from him."

A photograph of a boy with a dressed injury was included in the AIHRC report.

This boy was allegedly injured by Australian soldiers during a raid on his village. ( Supplied )

Another alleged victim was a farmer's son, Mohammad Wali, who was hit and beaten by the Australian soldiers, according to the Sarkhume residents and the AIHRC complaint file for the raid.

The file states "his testicles were squeezed" by the soldiers.

Hazratullah said Wali was deaf and could not understand commands from the soldiers when they detained him.

He was told that Wali was taken to the stable where he was beaten and had his testicles squeezed, Hazratullah told the ABC.

"He passed out a few times and didn't feel himself. He told them: 'I have got nothing (no information)'. They would squeeze his balls. He was shaking. He has a psychological problem now."

The AIHRC file stated that others — all of them innocent villagers — were detained and "hit with gun butts".

Villagers claim Australians apologised to locals for 'mistaken' raid

That afternoon the Australians left without providing any explanation for the raid.

The AIHRC complaint states that the Australians "took 11 people" away with them but released them after four days.

Lieutenant Colonel Jon Hawkins was the commander of the SOTG in Afghanistan at the time of the Sarkhume raid. ( Supplied: Department of Defence )

After the raid occurred, local authorities and the Australian military were besieged with complaints about the killings and assaults.

The then-commander of SOTG, Lieutenant Colonel Jon "Irish" Hawkins, defended the operation.

Lieutenant Colonel Hawkins, who did not participate in the raid, later described the claims of the Sarkhume locals as "some wild allegations".

He is the only senior special forces officer to discuss the raid publicly, if only briefly, during an interview for journalist Chris Masters's book on Australian special forces operations in Afghanistan, No Front Line.

Lieutenant Colonel Hawkins dismissed the allegations as coming from "hard tough, hard farmers who were probably Taliban".

He acknowledged that he attended a series of meetings with Afghans about the raid and that the Australian Defence Force Investigative Service (ADFIS) had conducted an inquiry into the matter, but said that ADFIS seemed to have little understanding of the "absolute chaos" of combat.

Masters wrote that when the Australians arrived at Sarkhume they saw "an Afghan male … moving evasively, and when challenged he raised a grenade" and was shot and killed.

The book states that another man was observed manoeuvring and carrying an AK-47 assault rifle and was also fired on and fatally wounded.

The meeting with Australians to discuss the raid is remembered by Sarkhume locals who said the only justification given for the operation was a claim that the Taliban was using their district to fire mortars or rifles.

They vigorously denied any such involvement and noted that the Australians were apologetic in the meeting.

Shaista said the Australians admitted they were "mistaken" and had "been misled".

He said the Australians never told them who had given them the information and nobody ever faced any justice over the killings.

"We told the Australians to hand over that person who passed the reports (implicating the village in Taliban activity)," said Abdul Latif.

Contacted by the ABC on September 18, Lieutenant Colonel Hawkins declined to comment, citing the fact an investigation into alleged war crimes in Afghanistan by Australian troops was currently being undertaken by the Assistant Inspector General of the Australian Defence Force (IGADF) Justice Paul Brereton.

The ABC understands that the Sarkhume raid is part of the investigation.

Civilians were killed: AIHRC

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.

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

When the ABC put questions to the Defence Department about the Sarkhume raid — including what evidence had been found confirming the dead men were armed — a spokesman said it was not appropriate for Defence to make any comment in order "to protect the integrity and independence of the IGADF inquiry and the reputations of individuals who might otherwise unfairly affected".

Further investigations into the Sarkhume case are supported by the AIHRC with the commission's chair Shaharzad Akbar telling the ABC: "The Afghanistan Independent Human Rights Commission has time and again repeatedly asked for the investigation of civilian casualties by all authorities from all sides."

She said the AIHRC stood by its report into the Sarkume raid, as she spoke for the first time about the killings.

"Our position remains the same. Civilians were harmed in this. The people who were killed were civilian. The seven people who were injured were civilians," she said.

Back in Sarkhume, residents said they have had no contact or have received no information relating to any investigations being undertaken in Australia, despite the heavy toll the raid took on their families.

"Even now when there is the noise of the aircraft, our children are crying," Abdul Latif said.

Among those most affected is Mirza Khan's mother.

She was home by herself during the raid when a soldier came to tell her to go to her son, said Shaista Khan.

"My mother's heart became heavy and [she] rushed to that land by the tower where my brother was lying. She prepared the body. There was no-one else."

Additional reporting by Bilal Sarwary