The HMAS Sydney, a Royal Australian Navy ship, was tied up to a dock at Naval Base San Diego on Tuesday, just south of the Coronado Bridge, not far from where a dead fin whale was tethered.
"The Royal Australian Navy can confirm that as HMAS Sydney was berthing alongside Naval Base San Diego in California, two deceased whales dislodged from her hull beneath the surface," the Australian Department of Defence communicated to NBC 7 in an email sent out Tuesday.
The whale carcass appeared to be between 30-40 feet long. The other fin whale was not visible on Tuesday.
It's unclear where the ship, which, according to the Australian Navy, is "equipped with advanced combat systems, providing the ship with layered offensive and defensive capabilities to counter conventional and asymmetric threats" -- came in contact with the marine mammals, though it is known that the ship tied up to the dock on Saturday morning.
The Sydney has been holding joint exercises with the U.S. Navy in the area since early April.
"The U.S. Navy and the Royal Australian Navy are cooperating with the NOAA Fisheries and other agencies to review the incident," the Australian Department of Defence said.
When NBC 7's Sky Ranger returned to the site in the afternoon, the carcass was gone, possibly towed far out to sea in the hopes that juvenile great whites, which have been spotted recently off San Diego shorelines, won't locate it in coastal waters.
"The navy takes marine mammal safety seriously and is disheartened this incident occurred," the Australian Department of Defense also stated in the email.
Ship strikes are also suspected in the deaths of a fin whale and two gray whales found last month in the San Francisco Bay Area, experts said.