Mr Morrison said while the accusations of war crimes by Australian troops are "disturbing", veterans deserve the nation's full support.
Prime Minister Scott Morrison has described a report into alleged war crimes committed by Australian soldiers in Afghanistan as "disturbing", but said the allegations must be dealt with by the Australian justice system.
The report conducted by Major General Paul Brereton, which was handed down on Thursday, revealed evidence that Australian special forces may have murdered at least 39 Afghan civilians or prisoners.
In his first comments since the long-awaited findings were made public, Mr Morrison described the alleged war crimes detailed in the report as “disturbing and distressing”.
"I think there has been a lot of courage shown by those who have come forward through this process, that would not have been easy," he said.
"This is a terrible, terribly disturbing and distressing report but the thing about Australia is we will deal with it. And we will deal with it under our law, under our systems, and our justice system."
The Inspector General of the Australian Defence Force (IGADF) has recommended 19 current and former personnel be prosecuted over the alleged war crimes, and that compensation be paid to Afghan victims and families.
When asked about compensation, Mr Morrison said: “There is nothing for me to comment on that matter. That is not a matter that is currently being considered by the government at this stage.”
In a statement on 19 November, the Afghan government said several Australian leaders, including the prime minister and ministers of foreign affairs and defence, "apologised to both the people and the Government of the Islamic Republic of Afghanistan for these violations, and assured the Government of Afghanistan of their compliance with the recommendations of the Afghanistan Inquiry, providing justice and compensation to the families of the victims".
"Both governments will work closely together to ensure that the recommendations of the Afghanistan Inquiry are met, justice is provided and compensation is paid to the victims," it said.
The prime minister said the justice process must "run its course".
“Those that you’ve charged with running the justice process are the ones who need to conduct those inquiries and make the judgments about how they deal with witnesses and what, if any, they put in place for those witnesses," he said.
“It is not appropriate for the government to involve itself in the course of that independent investigation, and in that case anymore than it with any other investigation that the Australian Federal Police might undertake."
Ahead of the report's release, Mr Morrison had warned Australians that it would contain "difficult and hard news".
On Saturday, he stressed that while the behaviour of a “small number” of soldiers was “disturbing”, it was important that other veterans weren’t tarnished by the findings.
“The other element I’ve been anxious about is ensuring that all our serving men and women and all those who’ve served in no way feel reflected upon by the alleged actions of a small number within our defence forces," he said.
“They have earned the respect which we rightly provide to them, and should.”
Asked whether he was concerned about reprisals against Australians in the wake of the findings, Mr Morrison said the government “took all the necessary precautions”.
“We ensured that between the time of the receipt of the report and the announcement of the findings, we engaged a lot with our overseas partners.
“There are always risks out there, and it’s always important Australia stays on the front foot to get ahead of these risks.”