The bodies of sailors missing since the destroyer the USS Fitzgerald collided with a container vessel have been found in flooded compartments in the damaged ship, the United States Navy says.

"As search and rescue crews gained access to the spaces that were damaged during the collision this morning [local time], the missing sailors were located," the US Seventh Fleet said in a statement.

The statement did not say if all seven missing crew members were found in the ship, however Japanese media reported that all seven had been found dead.

The sailors were reported missing after the guided missile destroyer USS Fitzgerald collided with a Philippine-flagged container ship south of Tokyo Bay in Japan yesterday.