The dead whales were dislodged from the hull of the HMAS Sydney as the destroyer was berthing alongside the San Diego naval base in California.

The two are believed to be fin whales - one was about 20 metres long, and the other was about 7.5 metres.

The Department of Defence 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 spokesperson told AAP on Wednesday.

The San Diego naval base has secured the whale carcasses with booms until they can be removed from the harbour.

Greens senator Peter Whish-Wilson said their deaths should not be in vain.

"This is a timely reminder of our impacts on the oceans and precious marine life," he said.

"Ship strikes often go unreported and undetected. We must learn from this so we're better informed to prevent such devastating events from happening in the future."

The HMAS Sydney is 146 metres long, with its hull extending more than seven metres below the surface.

The warship has a top speed of 28 knots and is crewed by about 180 sailors.

The vessel is primarily used for air defence, surface and undersea warfare and surveillance.

Whale strikes are common off the coast of California, with one research biologist telling local media there are about 50 incidents every year.

John Calambokidis said the latest incident was sad but not surprising.

"In the vast majority of cases I'm familiar with, the ship is unaware of having struck the whale," he told ABC 10News San Diego.

Mr Calambokidis said fin whales were particularly vulnerable to ship strikes because of their size and the amount of time spent near the surface.

Australian Associated Press