The Navy on Tuesday announced the removal of Capt. John Banigan, saying the action was based on findings of an investigation into the poor command climate aboard the USS Lake Erie.
Officials would not elaborate, saying the case is still under investigation. Banigan could not be reached for comment.
Banigan has been temporarily assigned to the staff of commander of the Naval Surface Force of the U.S. Pacific Fleet.
He had commanded the guided-missile cruiser since May 2013.
Capt. Douglas Kunzman has been temporarily assigned to command the ship.