"We've discontinued the search and rescue", said Vice Adm. Joseph Aucoin, the commander of the USA 7th Fleet.
The sailors were reported missing after the USS Fitzgerald collided with the Philippine-flagged ACX Crystal in the early hours of June 17, sustaining what Aucoin said was a "big gash" below the waterline on the starboard side.
The container ship has berthed at Tokyo's Oi wharf, where officials have begun questioning crew members about the cause of the crash.
The 154-metre (500-foot) Fitzgerald - commissioned in 1995 and deployed in the Iraq war in 2003 - was pulled by a tugboat back to its base on Saturday in Yokosuka, southwest of Tokyo.
The Philippine Embassy in Tokyo, said DFA, will continue to coordinate with Japanese authorities. Images show that the ship had taken on massive amounts of water. Two other crew members suffered cuts and bruises and were also flown out by helicopter.
The Fleet said the sailors were found as search and rescue crews gained access to the spaces that were damaged in the collision, and the sailors were found in flooded berthing compartments. Bryce Benson, the Fitzgerald's commanding officer, who is in a stable condition in hospital.
DAMAGED part of USS Fitzgerald is seen at the U.S. naval base in Yokosuka, Japan yesterday.
It was unclear how the collision happened.
"Once an investigation is complete then any legal issues can be addressed", a spokesman for the U.S. 7th fleet told the Guardian.
USA aircraft is assisting in the effort, along with several Japanese helicopters and one plane, the 7th Fleet said.The area is particularly busy with sea traffic, said Yutaka Saito of the coast guard. A total of seven sailors had been missing since Saturday's crash off Japan's coast.
"The search and rescue is over", U.S. 7th Fleet commander Vice Admiral Joseph Aucoin told reporters Sunday.
"It's been a tough day for our Navy family".
USA and Japanese aircraft and surface vessels continued the search after the Fitzgerald sailed into the port of Yokosuka south of Tokyo.
The Navy advises that the deceased sailors have been transferred to Naval Hospital York Yokosuka ready for identification. Yoko Kato, a spokeswoman for the US Navy in Yokosuka, said not all seven were recovered. "All of our thoughts and prayers are with the Fitzgerald crew and their families", said Adm. John Richardson, Chief of Naval Operations.
Shortly after the collision the USA made a request for support from the Japanese Coast Guard, which was the first on scene and continues to be the lead for search-and-rescue efforts, according to a release. Nippon Yusen said it was co-operating with the investigation.
"Heroic efforts prevented the flooding from catastrophically spreading, which could have caused the ship to founder or sink", Aucoin added.