Australia's top military officer has admitted there was credible evidence that his special forces unlawfully killed at least 39 Afghanistan civilians and prisoners, recommending the matter be taken up by a prosecutor investigating alleged war crimes.

"Some patrols took the law into their own hands, rules were broken, stories concocted, lies told and prisoners killed," said Chief of the Defence Force General Angus Campbell.

His comments came as the result of a damning years-long investigation into the military's behaviour in Afghanistan were published.

General Campbell "sincerely and unreservedly" apologised to the people of Afghanistan and said the 25 Australian special forces accused of wrongdoing in 23 incidents had brought a "stain" on their regiment, on the armed forces and on Australia.

General Angus Campbell

"This shameful record includes alleged instances in which new patrol members were coerced to shoot a prisoner in order to achieve that soldier's first kill, in an appalling practice known as 'blooding'," he said.

General Campbell called for some distinguished service medals awarded to special operations forces who served in Afghanistan between 2007 and 2013 to be revoked.

Large chunks of the 531-page report were redacted because of classified security information or because they contained material that could compromise future criminal proceedings.

After the 11 September, 2001 terror attacks more than 26,000 Australian uniformed personnel were sent to Afghanistan to fight alongside US and allied forces against the Taliban, Al-Qaeda and other groups.

Australian combat troops left the country in 2013, but since then a series of often-brutal accounts have emerged about the conduct of elite special forces units.

They range from reports of troops killing a six-year-old child in a house raid to a prisoner being shot dead to save space in a helicopter.

Australia's government attempted to cushion the blow of the report, with Prime Minister Scott Morrison telling Australians last week to brace for the "honest and brutal truths" contained within the redacted document.

Mr Morrison also called his Afghan counterpart yesterday to foreshadow "some disturbing allegations" that the government was taking "very seriously".

Last week, Mr Morrison announced the appointment of a special investigator to prosecute the alleged war crimes, a move aimed at forestalling any prosecution at the International Criminal Court.

An independent panel was also set up to drive cultural and leadership changes within the armed forces.

Australia's government had previously spent years trying to suppress whistle-blower reports of the alleged wrongdoing, with police even investigating reporters involved in bringing those accounts into the light.

The matter first came to public attention in 2017 when public broadcaster ABC published the so-called "Afghan files", which alleged Australian troops had killed unarmed men and children in Afghanistan.

In response, Australian police launched an investigation into two ABC reporters for obtaining classified information - even raiding the broadcaster's Sydney headquarters last year, before dropping the case.