USS Dewey and several U.S. Navy aircraft, joined the Japanese Coast Guard and Japan Maritime Self-Defense Force helicopters, ships and aircraft to search for the missing sailors.
With the assistance of US Navy tug boats, USS Fitzgerald managed to return to the its base in Yokosura, despite serious starboard side damage during the crash.
The early Saturday morning collision with a Philippines-flagged merchant ship caused extensive damage to the USS Fitzgerald, a guided-missile destroyer, and left seven of its crew members unaccounted for. The bodies were found in flooded berthing compartments after divers were able to reach the areas, the Fleet said.
The Navy said the dead U.S. crew were found by the divers. Two berthing spaces, a machinery room and the radio room were damaged and began taking in water after the destroyer was rammed mid-right side of the ship.
The victims might have been killed by the impact of the collision or drowned in the flooding, said Navy spokesman Lt Paul Newell, who led the media on a visit to get a firsthand look at the mangled destroyer.
But questions remained over how the collision occurred on a clear night a few miles off the coast south of Yokosuka and Tokyo.
The Navy said that the families were being notified and provided the support they need during "this hard time".
The names of the dead sailors will not be released until after their families have been identified.
The 500-foot Fitzgerald was pulled by a tugboat back to its base on Saturday, where divers searched the damaged areas of the destroyer that was deployed in the mid-90s.
Australia suspends air strikes in Syria after US downing of Syrian jet
Earlier this month , the US shot down another pro-regime drone in the same area after it dropped munitions near coalition forces. Sharif says the missile launch reflects Iran's "military power" though Iran has no intention of starting another war.
Seven crew members were unaccounted for after the collision flooded berths with seawater.
"This has been a hard day", Joseph P Aucoin, the commander of the Seventh Fleet, said before the announcement that the bodies had been found.
The Fitzgerald is based in Yokosuka and has a crew of approximately 330 sailors.
In 2007, Benson screened for the early command program and later served as the executive officer, then as commanding officer of the USS Guardian, deployed from Sasebo, Japan, from 2008 to 2010.
The ship's captain Commander Bryce Benson was airlifted to hospital in Yokosuka after dawn on Saturday with a serious head injury. It was unclear how many others may have been hurt.
The Japanese coast guard questioned crew members of the ACX Crystal, and is treating the incident as a case of possible professional negligence, said Masayuki Obara, a regional coast guard official.
Sykes says her son told her that sailors initially believed they were under attack and some immediately went to man the guns.
The damage to the destroyer suggests that the container ship, the ACX Crystal, might have slammed into it at a significant speed.
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