The pilot ejected from the F/A-18E Super Hornet before impact at about 10:00 pm yesterday (0500 GMT today) and was in stable condition aboard the USS Carl Vinson, the Navy said in a statement.
The other aircraft operating at the time of the accident were diverted to the Coronado naval base in California, where they landed without incident an hour after the crash, it said.
The F/A-18E Super Hornet was not recovered.
Another US military aircraft crashed yesterday in California, local media reported. The pilot of the Marine Harrier jet ejected for reasons that were not yet clear, and the aircraft crashed in a residential area. No one was hurt.