The Department of Defence has revealed for the first time that an Australian soldier fired on a crowd of demonstrators during a chaotic and deadly protest outside an Australian base in Afghanistan.

Key points: An Afghanistan Human Rights Independent Commission investigation writes that five or six people died in a violent protest on a military base in the Uruzgan Province

An Afghanistan Human Rights Independent Commission investigation writes that five or six people died in a violent protest on a military base in the Uruzgan Province At the time of the incident in 2010, NATO reported only one protester had died in the clash

At the time of the incident in 2010, NATO reported only one protester had died in the clash Defence has confirmed an Australian soldier fired on the crowd in "self-defence"

The admission came after the ABC obtained a report from the Afghanistan Independent Human Rights Commission (AIHRC) that stated five civilians had been killed and six wounded during the protest near the forward operating base in Uruzgan province in 2010.

At the time, NATO claimed only one protester was killed when he "aimed an AK-47" at foreign troops inside the base and that he was shot by an International Security Assistance Force (ISAF) service member.

But after the ABC asked Defence about the AIHRC's report of a higher civilian death toll, a spokesperson confirmed an Australian soldier shot at protesters.

"Coalition soldiers, including an Australian, engaged the protesters in self-defence," the spokesperson said.

"An investigation by the Commanding Officer into the incident found that Australian and ISAF soldiers acted appropriately and in accordance with their Rules of Engagement."

Reports at the time said the protest was sparked by false rumours that foreign forces at the base had been burning copies of the Koran.

The fatal protest is another incident that suggests some civilian casualties associated with Australian operations in Uruzgan were not fully reported or investigated at the time.

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

Another ABC investigation last week contained new allegations of violence by the Australian special forces, including claims some soldiers killed unarmed civilians and twisted a young man's testicles.

The 'Chora Rock Show'

The ABC has obtained more than 90 investigation files compiled by the Uruzgan office of the AIHRC, with one of the reports focusing on the protest at Forward Operating Base Mirwais in the Chora Valley on September 17, 2010.

Footage of three minutes of the clash obtained by the ABC shows what was happening from an Australian watch post on the perimeter of the military base, about 20 kilometres north-east of the provincial capital Tarin Kot.

The first minute shows hundreds of men and boys approaching the base, with some running and waving sticks.

"The group has a mixture of black and white flags and appears to be about the same size in number, possibly five to seven hundred," a crouching Australian soldier reports over the radio in the video.

"Jesus! Heads up! Coming in! F***ing hell," shouts another digger.

The sound of dozens of rocks bouncing off the tin roof of the outpost can be clearly heard on the video, while others can be seen landing in the post.

"Thank f*** for helmets," a soldier can be heard saying.

As a soldier grabs smoke-grenades, another report is radioed out: "We've taken cover behind a wall … we're going to throw smoke … in an attempt to disperse the rock throwing. Over."

The footage ends, with no shots fired by the Australian soldiers.

What happened after the footage finishes and why the Afghan people attacked the military base is not clear cut.

There is no suggestion by the ABC that any of the soldiers in the video opened fire or were responsible for the protester casualties that day.

The clash was later dubbed the "Chora Rock Show" by Australian troops.

Coalition forces engaged in 'self-defence'

The ABC understands protesters, egged on by suspected Taliban sympathisers, tried to smash their way into the base, prompting some troops inside the base to open fire at the crowd.

"The breaching of the perimeter gate by armed protesters would have created an extremely dangerous and unpredictable situation that would have threatened the lives of Australian soldiers and likely have resulted in more deaths," Defence said in its statement to the ABC.

Asked by the ABC whether any Australian troops had opened fire with live rounds during the protest, Defence said: "Coalition soldiers, including an Australian, engaged the protesters in self-defence."

"Coalition rounds were fired towards the protesters after weapons were observed in the rioting crowd, and the assessment that the perimeter gate was under imminent threat of being breached and that their lives were in immediate danger. Their fire caused the crowd to move away from the gate. A Defence investigation at the time of the incident was unable to confirm fatalities."

At the time of the incident, the Australian Defence Force issued a statement saying that Australian troops, coalition forces and members of the Afghan National Army had helped defend the base.

The statement said one protester aimed an AK-47 at one of the coalition soldiers, who then shot the protester.

The NATO-led International Security Assistance Force also issued a statement that said an ISAF service member shot the man in accordance with the rules of engagement.

The ABC tracked down the then-ISAF public affairs officer, James Judge, who responded to media queries about the incident at the time.

Mr Judge, who now runs his own public relations firm in the United States, said any statement would have been "based on the information available at the time".

"I was providing a quote same day with info that could have changed, but I'm pretty sure I would have remembered a discrepancy that large and we would have… made an effort to correct any inaccurate information that would have been provided."

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Reporting did not always match reality: Kolomeitz

Reports of a higher casualty toll were later acknowledged by an Australian diplomat who was on the base at the time.

In his book The Dust of Uruzgan, Department of Foreign Affairs and Trade staffer Fred Smith wrote that he was later told by NGO workers that there had been a higher death toll than that first reported.

Contacted in Canberra, Mr Smith declined to comment.

Commenting on the AIHRC Chora protest report, former Australian army legal officer with the Special Operations Task Group, Glen Kolomeitz, said concerns that official reporting from ISAF did not match the reality on the ground were well founded.

Mr Kolomeitz, who was deployed to Uruzgan in 2010, said he had received some reports from the International Committee of the Red Cross that provided more detail about civilian casualty incidents than that being provided by NATO or ISAF sources.

"There were a lot of allegations that I hadn't heard through NATO or ISAF sources," he said.