Under the museum's half-a-billion dollar expansion, the report will be among 1200 items in the Afghanistan gallery which officially opens in June.
The Brereton report was publicly released in late 2020 and found credible information Australian special forces soldiers murdered 39 Afghan civilians and prisoners in 23 incidents.
One redacted incident was described in the report as "possibly the most disgraceful episode in Australia's military history".
Speaking in an SBS documentary about the war memorial's redevelopment, director Matt Anderson said the Afghanistan gallery would include the more "difficult elements" of Australia's story in the war-torn country.
"The Australian memorial must acknowledge the fact of the Brereton report," he said.
"I know from my own time in Afghanistan, 18 months of my life, that the men and women that I served with, some of them say, 'mate, you can't put it in here', because that will cover and cloud in their minds, their service and their sacrifice.
"I've had others who say they won't visit the memorial if I don't put it in, so what I need to do is to put it into context."
Mr Anderson said the Afghanistan inquiry found the special operations task group had overwhelmingly served with skill and courage.
"I want people who visit the galleries to understand that outcome of the Brereton report and I want anyone who visits the Afghanistan gallery to understand the nature of that service over those 20 years, and as a nation and as a veteran to be justifiably proud of that service," he said.
Victoria Cross recipient Ben Roberts-Smith has been charged with five counts of war crime murder, alleged to have been committed during his service in Afghanistan as a special forces soldier between 2009 and 2012.
He denies the accusations and remains on bail.
The Afghanistan gallery is the last to be completed of the renovated Anzac Hall and does not include the altered display of Roberts-Smith following his arrest over alleged war crimes.
A panel in the memorial's Hall of Valour, which accompanies the decorated soldier's uniform and medals, now includes information about his arrest that notes the "legal process is ongoing".
The Brereton report will also be displayed in addition to a copy of the post-World War Two Geneva Conventions that establish humanitarian treatment during conflicts, and a card directing Australian troops about lawfully opening fire and detention.
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