An inaccurate version of the Australian flag was flown at a burial ceremony for Australian World War I soldiers in northern France last month.
The Veterans Affairs Department has confirmed problems with the flag involved one of the stars on the Southern Cross being in the wrong place.
It also had the Union Jack upside down and was a different shape.
The department says the problem is a matter for the Army, which conducted the ceremony in Fromelles.
The federal opposition wants an explanation
Veteran's affairs spokeswoman Louise Markus says the Minister for Veterans Affairs was at the event, representing the Government.
"He needs to be able to explain why a flag that was not our Australian flag was flown as if it was."
The ABC reports the soldiers were killed in the Battle of Fromelles in 1916 during World War I. Their remains were found in a mass grave in 2008.
The first of 250 unknown British and Australian soldiers were reburied last month.