In a statement to the ABC, the Australian Department of Defence confirmed that "as HMAS Sydney was berthing alongside Naval Base San Diego in California two deceased whales dislodged from her hull beneath the surface".
The department said the Australian and US navies were cooperating with local marine authorities and other agencies to review the incident.
"The navy takes marine mammal safety seriously and is disheartened this incident occurred," a Defence spokesperson said.
Naval Base San Diego has secured the whale carcasses with booms until they can be removed.
