Australia's special forces are accused of unlawfully killing 39 Afghanis and "blooding" younger recruits by demanding they murder civilians and plant evidence on their bodies to cover up the alleged crimes.

A bombshell report into allegations of serious misconduct by Australian soldiers in Afghanistan has disclosed multiple allegations of unlawful killings by or involving Australian Defence Force members and the cruel treatment of some prisoners of war.

Chief of the Defence Force General Angus Campbell called the allegations "deeply disturbing".

It also finds that the prevalence of rumours of the use of dogs to inflict injuries on foreign nationals in some instances suggest it is likely to have occurred.

The report recommends that the Chief of the Defence Force refer 36 matters to the Australian Federal Police for criminal investigation. Those incidents involve 23 incidents and involve 19 individuals.

"The nature and extent of the misconduct allegedly committed by ADF members on operations in Afghanistan is very confronting,'' Inspector-General of the Australian Defence Force JM Gaynor writes in the transmittal letter to the Chief of Defence Force Angus Campbell.

"The Report discloses allegations of 39 unlawful killings by or involving ADF members. The Report also discloses separate allegations that ADF members cruelly treated persons under their control.

"None of these alleged crimes was committed in the heat of the battle. The alleged crimes were non combatants or no longer combatants."

The report follows a four-year inquiry examining the conduct of the special forces in Afghanistan that interviewed 423 witnesses and reviewed more than 20,000 documents and 25,000 images.

War crimes are defined as the murder and cruel treatment of non-combatants and persons that are seriously wounded, been captured or are prisoners of war.

In 28 instances, the inquiry has found rumours allegations and suspicions of a breach of Law of armed conflict are not substantiated.

"However, the inquiry has found that there is credible information of 23 incidents of which one of more non-combatants or persons hors-de-combat were unlawfully killed by or at the direction of members of the Special Operations Task Group in circumstances which, if accepted by a jury, would be the war crime of murder, and a further two incidents in which a non-combatant or persons hors-de-combat was mistreated in circumstances which, if so accepted, would be the war crime of cruel treatment.

"Some of these incidents involved a single victim, and some multiple victims."

Those incidents involved a total of 39 individuals killed, and a further two cruelly treated; and a total of 25 current or former Australian Defence Force personnel who were perpetrators either as principals or accessories, some of them on a single occasion and a few on multiple occasions."

"None of these incidents of disputable decisions made under the pressure of the heat of the battle,'' the report states.

"The cases in which it has been found that there is credible information of a war crime are ones in which it was or should have been plain that the person killed was a non-combatant. While a few of these cases are cases of Afghan local nationals encountered during an operation who were of no reasonable view participating in hostilities, the vast majority are cases where the persons were killed when hors-de-combat because they had been captured and were persons under control, and as such were protected under international law, a breach of which is a crime."

Australians Special Operations Task Group soldiers in Afghanistan, 2012. Photo / Department of Defence

In highly disturbing allegations, the report finds SAS soldiers 'planted' incriminating weapons on civilians and others that they unlawfully killed to fake evidence to conceal deliberate unlawful killings.

"The Inquiry also found that there is credible information that some of the members of the Special Operations Taskforce carried 'throwdowns' foreign weapons or equipment, typically though not invariably easily concealable such as pistols, small hand held radios (ICOMs), weapon magazines and grenades - to be placed with the bodies of 'enemy killed in action' for the purposes of site exploitation photography, in order to portray that the person killed had been carrying the weapon or other military equipment when engaged and was a legitimate target,'' the report states.

"In different Special Operations Task Group rotations the Inquiry has found that there is credible information that junior soldiers were required by their patrol commanders to shoot a prisoner in order to achieve the soldiers first kill, in a report known as 'blooding','' the report states.

The Afghanis unlawfully killed would be 'under control' and a prisoner of the Australian soldiers and not at risk of flight.

"Typically, the patrol commander would take a person under control and the junior member, would then be directed to kill the person to kill the person under control.

"Throwdowns would be placed with the body and a cover story created. This was reinforced with a code of silence."

The report finds that younger soldiers complied with the requests.

"Subordinates complied for a number of reasons. First, to a junior Special Air Service Regiment trooper, the patrol commander is a 'demigod' who can make or break the career of a trooper,'' the report states.

"Secondly, to such a trooper, who has invested a great deal in gaining entry into the SASR, the prospect of being characterised as a lemon and not doing what was asked of them was a terrible one."

The genesis for the report according to the inquiry were "persistent rumours of criminal or unlawful conduct" by the Special Operations Task Group (SOTG) that prompted a call for an investigation by the Chief of the Army.

In January 2017, the inquiry commenced, with the inquiry broadened to all SOTG deployments in Afghanistan from the period of 2007 to 2016.

Australia's Prime Minister Scott Morrison spoke overnight with Afghanistan's President Ashraf Ghani ahead of the release of the report.

But in an unfortunate "miscommunication", Morrison denied expressing his "deep sorrow" as claimed by the Afghani government.

Around 2:47am Australian time, the official Twitter account of the Office of the President of Afghanistan confirmed the phone call.

"In this telephone call, the Prime Minister of Australia expressed his deepest sorrow over the misconduct by some Australian troops in Afghanistan and assured the President of the Islamic Republic of Afghanistan of the investigations and to ensuring justice,'' the statement said.

"Also, Senator the Hon Marise Payne, Minister for Foreign Affairs of Australia in a letter to the Minister of Foreign Affairs of Afghanistan has extended apologies for the misconduct identified by the inquiry, by some Australian military personnel in Afghanistan.

"The letter reads, "The Australian Minister for Defense, Senator the Hon Linda Reynolds CSC and the Chief of the Defense Force, General Angus Campbell AO DSC, are now considering the inquiry's extensive findings and recommendations and will make public statements subsequently."

Exactly seven days ago, the Morrison warned the nation to prepare for allegations of "serious and possibly criminal conduct" by Australia's defence force in Afghanistan that could see soldiers prosecuted for unlawful killings.

A special investigator will be appointed to consider allegations of war crimes by Australia's soldiers in the Middle East following the completion of a long-running defence investigation into the claims.

"This is going to be very difficult for Australians. It is going to be very difficult for our serving community and our veterans community,'' Morrison said.

"It is going to be difficult for all of us. But what we are seeking to do, as a government, I think what we have to do as a country, is to absorb this in a way that enables us to uphold the integrity of our justice system and uphold the integrity of our defence forces. We rely vitally on both of these institutions, absolutely vitally.

"Given the likely allegations of serious and possibly criminal misconduct, the matters raised in the inquiry must be assessed, investigated and where allegations are substantiated, prosecuted in court. To undertake this role, the government is establishing the Office of the Special Investigator."

Defence Minister Linda Reynolds confirmed the scandal could involve stripping soldiers of medals if misconduct is proven and they are ultimately convicted of crimes.

She stressed that 39,000 Australians had served in Afghanistan and the report in "no way" undermined the work of the vast majority of these soldiers.

"They served with great distinction and 41 Australians lost their lives in that process,'' she said.

"Today we have, as minister, I could not be prouder of the work our men and women are doing on bushfire and Covid-19 assist.

Morrison said the unredacted report made for disturbing reading. A redacted version is expected to be released by the Australian Defence Force.

"There is some disturbing conduct here, but we cannot then take that and apply it to everyone who has pulled on a uniform and if we did this, that would be grossly unjust, grossly unjust,'' the Prime Minister said.

"I know that wouldn't be the view of people here or in government or anywhere else. We all share a deep respect for our defence forces, but we also share a deep respect for justice. It is about managing those two issues to the highest standards I think we place on them in Australia."

Australia's most decorated living soldier Ben Roberts-Smith has confirmed his own conduct is being investigated but has strongly denied wrongdoing.

The SAS hero was awarded the Victoria Cross in 2011 for bravery under fire during his fifth tour of Afghanistan.

In a statement last week, Roberts-Smith said he welcomed the appointment of a special investigator to test the claims.

"It is regrettable that the IGADF Inquiry took such an extraordinarily long time to be finalised,'' he said.

"While I appreciate the complexity of the task ahead for the Special Investigator, I am hopeful that this next phase will be completed as expeditiously as possible so that all the current and former special forces soldiers who have been deeply impacted by the Inquiry process can move on with their lives."

The 42-year-old former soldier, who left the Army as a Corporal in 2013, is involved in a long-running defamation case involving Fairfax and the Nine network.

Fairfax media first reported in July, 2018, that Roberts-Smith was "one of a small number of soldiers subject to investigation by an inquiry looking into the actions of Australian special forces soldiers in Afghanistan."

The newspapers claims cover his service in Afghanistan between 2009 and 2012, including an allegation that he kicked an Afghan civilian named Ali Jan off a cliff. The injured man was later shot and died.

During the defamation hearings, Nine detailed two new allegations implicating Roberts-Smith in the execution of two Afghan prisoners during SASR missions in August and October 2012.

Roberts-Smith told The Australian newspaper in June that he also denied these claims and accused Fairfax of changing their story on the death of Ali Jan.

The Morrison Government has expressed concern that the release of the report could impact on the mental health of former and serving soldiers.