Cmdr. Adam Ochs was relieved of his duties as commanding officer of the USS Santa Barbara due to a "loss of confidence," the Navy announced.
The "provocative move," as the DOD called it, comes several days after the U.S. said it struck a Venezuelan drug-carrying vessel, killing 11 on board.
The three amphibious ships, which the Navy says are carrying more than 4,500 sailors and Marines, could be seen leaving Norfolk on Sunday.
U.S. Navy crews and the Japan Coast Guard fought the blaze for about 11 hours before extinguishing it Thursday morning.
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