USA 7th Fleet Vice Admiral Joseph P Aucoin said the search was continuing in a statement released almost 24 hours after the USS Fitzgerald, an Aegis guided missile destroyer, collided with the much larger Philippine-flagged merchant vessel 56 nautical miles southwest of Yokosuka.
Cmdr. Ronald Flanders of the U.S. Naval Forces Japan said the focus right now is on the families.
The bodies of the sailors are now being transferred to a naval hospital on US soil where they will be identified and at that point, their names will be released.
A member of the U.S. Navy Damage Control Training Team is seen near the U.S. national flag on the Arleigh Burke-class guided-missile destroyer USS Fitzgerald, at the U.S. naval base in Yokosuka, south of Tokyo, Japan, on Sun., June 18, 2017.
They were not injured and, apart from dents and scrapes on the left bow, there was little sign of damage to the ship.
The USS Fitzgerald being escorted to its mother port, the US Naval Base Yokosuka.
"This has been a hard day", said Vice Adm. Joseph Aucoin, commander of the U.S. Navy's 7th Fleet.
In the middle of the night, a Filipino container ship - nearly three times the size of the destroyer - crashed into the side of the Fitzgerald. Aucoin said the Fitzgerald is salvageable but that repairs will likely take months.
We set up a USS Fitzgerald Emergency Family Assistance Center within hours, and disseminated the phone numbers to their hotlines through social media and Navy websites. Bryce Benson, suffered a head injury in the collision and was airlifted to the U.S. Naval Hospital in Yokosuka.More news: Jared Kushner speaks at tech event
U.S. President Donald Trump thanked Japan for its help in the search.
Seven sailors were reported missing when the collision happened, but not all of those missing were recovered, US Navy spokeswoman Yoko Kato said.
The crew, he continued, navigated the Fitzgerald into one of the busiest ports in the world with a magnetic compass and backup navigation equipment. The Navy said earlier the ship had about 300 crew on board.
Marine traffic records suggest the ACX Crystal, a 222-meter Filipino-flagged container ship, made a sudden U-turn roughly 25 minutes before the crash. The weather was clear with a swell of about 1.8m at the time.
Aucoin wouldn't speculate on the cause of the collision and would order a thorough investigation.
The USS Fitzgerald could have foundered, or even sunk, but for the crew's desperate efforts to save the ship, he said. The two damaged berthing compartments house a combined 116 crew members, Aucoin said.
The navy and coastguard are conducting separate investigations, but the Japanese side will ask for U.S. cooperation in its inquiries, a spokesman for Japan's transport safety board told AFP.
Aucoin described how the crew of the Fitzgerald had scrambled to keep the ship afloat after it collided with the larger cargo vessel, the ACX Crystal, which is registered in the Philippines.
Nippon Yusen, the Japanese shipping company that operates the container ship, said in a statement it is collaborating with the ship owner and fully cooperating with the investigation by the coast guard.