Up to 83 Syrian soldiers that had been fighting ISIS militants were reportedly killed in the air strikes around the Deir Ezzor military airport in Eastern Syria, ABC news Australia reported.
"Australian aircraft were among a number of international aircraft taking part in this Coalition operation," the Defense Department said in a statement.
"Australia would never intentionally target a known Syrian military unit or actively support ISIL. Defense offers its condolences to the families of any Syrian personnel killed or wounded in this incident."
The Russian military earlier said two F-16s and two A-10 jets that flew into Syrian airspace from neighboring Iraq carried out the actual attack. Neither type is listed as being in operation with the RAAF.
The strikes came less than a week into a fragile ceasefire aimed at stopping the bloodshed in Syria, as Russia accused militant groups of causing the truce to fail.