Navy and Marine Corps divers had been searching in flooded compartments of the destroyer for days after the damaged ship docked in Singapore. The cause of the Aug. 21 collision is under investigation.
The crash ripped a gash in the McCain’s hull, flooding crew berths and machinery and communications rooms.
The commander of the Navy’s Japan-based 7th Fleet was fired last week after a series of accidents this year raised questions about its operations. The firing of Vice Adm. Joseph Aucoin, a three-star admiral, was a rare dismissal of a high-ranking officer for operational reasons.
WATCH: Navy confirms remains found in flooded compartment on USS John McCain
The Navy also ordered an operational pause for its fleets worldwide to make sure all steps are being taken to ensure safe and effective operations. The Pacific Fleet will also carry out a ship-by-ship review of its vessels, looking at navigation, mechanical systems, bridge resource management and training.