A shocking Australian military report into war crimes has found evidence that elite Australian troops unlawfully killed 39 Afghan prisoners, farmers and civilians.

Australian Defence Force Chief Gen. Angus Campbell the shameful record included alleged instances in which new patrol members would shoot a prisoner in order to achieve their first kill in a practice known as "blooding." He said the soldiers would then plant weapons and radios to support false claims the prisoners were enemies killed in action.

Campbell told reporters in Canberra the illegal killings began in 2009, with the majority occurring in 2012 and 2013. He said some members of the elite Special Air Service encouraged "a self-centered, warrior culture."

The chief was announcing the findings of a four-year investigation by Maj. Gen. Paul Brereton, a judge and Army reservist who was asked to look into the allegations and interviewed more than 400 witnesses and reviewed thousands of pages of documents. Brereton recommended 19 soldiers be investigated by police for possible charges, including murder.

"To the people of Afghanistan, on behalf of the Australian Defence Force, I sincerely and unreservedly apologize for any wrongdoing by Australian soldiers," Campbell said.

He said he'd spoken directly to his Afghan military counterpart to express his remorse.

"Such alleged behavior profoundly disrespected the trust placed in us by the Afghan people who had asked us to their country to help them," Campbell said. "It would have devastated the lives of Afghan families and communities, causing immeasurable pain and suffering. And it would have put in jeopardy our mission and the safety of our Afghan and coalition partners."

As well as the 39 killings, the report outlines two allegations of cruel treatment. It says that none of the alleged crimes were committed during the heat of battle.

Only parts of the report have been made public. Many details, including the names of alleged killers, remain redacted.

The report said a total of 25 current or former troops were involved as perpetrators or accessories in 23 separate incidents, with some involved just once and a few multiple times.

It said some Australian troops would regularly carry "throw downs" - things like foreign pistols, radios and grenades that they could plant on those they killed so the Afghan civilians would appear like combatants in photographs.

The report said most of the alleged crimes were committed and concealed at a patrol commander level by corporals and sergeants, and that while higher-level troop and squadron commanders had to take some responsibility for the events that happened on their watch, they weren't primarily to blame.

The report paints a picture of a toxic culture in which soldiers were competing against those from other squadrons, accounts of deaths were sanitized or embellished, and many procedures to ensure safety and integrity had broken down.

"Those who wished to speak up were allegedly discouraged, intimidated and discredited," Campbell said.

The report recommended 19 soldiers be referred to federal police for criminal investigation. Campbell said he's accepting all the report's recommendations.

Australian Prime Minister Scott Morrison has already announced a special investigator will help pursue possible prosecutions because the workload would overwhelm existing police resources.

Many troops are also likely to be stripped of their medals and the defense force will undergo significant structural changes. The report says that where there is credible evidence of unlawful killings, Afghan families should be compensated immediately by Australia without waiting for the criminal cases to proceed.

"This will be an important step in rehabilitating Australia's international reputation, in particular with Afghanistan, and it is simply the right thing to do," the report states.

Prior to the report's release, announced a new investigative agency to build criminal cases against Australian special forces suspected of committing war crimes in Afghanistan.

The Office of the Special Investigator is to be formed after a four-year investigation into allegations and rumors surrounding behavior of some soldiers in Special Air Service and Commando Regiments in Afghanistan from 2005 and 2016.

Benjamin Roberts-Smith, Australia's most highly-decorated member of the armed services when he left the SAS in 2013, has been accused by former colleagues of unlawful treatment of prisoners including illegally killing prisoners. The former corporal, who was awarded the Victoria Cross and the Medal for Gallantry for his service in Afghanistan, has denied any misconduct.

Prime Minister Scott Morrison said the new agency, headed by a retired judge or senior criminal lawyer, was needed because the workload would "seriously overwhelm" existing police resources.

"This report will be difficult news and all of our partners must be assured and those around the world who rightly hold the Australian Defense Forces in high regard," Morrison told reporters.

"In Australia, we deal with this stuff and we deal with it honestly, but in accordance through the rule of law and by following the justice practices and principles that makes Australia what it is," he added.

Two Australian Broadcasting Corp. journalists until recently faced potential prison sentences for using leaked classified defense documents as a basis for a 2017 report that detailed allegations of Australian soldiers killing unarmed men and children.

Police raided ABC Sydney headquarters with search warrants last year but prosecutors decided that charging the journalists would not be in the public interest.

Prosecuting alleged Australian war criminals is expected to take years.

"These are incredibly complex events involving actions and conduct in another country, in a war," Morrison said.

"This is not a simple matter ... and so it will take as long as it needs to take to ensure we deal with our dual objectives of addressing the justice that is necessary in accordance with our laws and systems but also ensuring the integrity of our defense forces on which we all rely," he added.

Neil James, chief executive of the Australian Defense Association think tank, said the Australian military wanted soldiers to have their day in court to end a "continuous rumor mill."

"It's certainly the case that they're going to take a long time because we're talking about a complex investigation, witnesses will have to be interviewed under caution, in many cases those witnesses will be overseas, and in some cases it'll be hard to interview them because they are in enemy-held territory in a war zone," James said.

"So the complexity of this is going to be difficult, but it's got to be faced because . Australia has to face up to this, that things did go wrong and we need to fix it," he added.

Around 39,000 Australians served in Afghanistan and 41 were killed.

From AP