"This was not a small collision", Vice Adm. Joseph P. Aucoin, commander of the Navy's Seventh Fleet, said at a news conference.
The names of the sailors will be released after families are notified, the Navy said. The ships collided at about 2:20 a.m. Saturday, when the Navy said most of the 300 sailors on board would have been sleeping.
According to reports, the crash caused the Fitzgerald to cave in about a third of the way back, causing significant damage.
The navy said the remains are being transferred to Naval Hospital Yokosuka where they will be identified. He spoke with the docked Fitzgerald behind him, after tugboats towed it ashore in the hours after the collision 104 kilometers southwest of Yokosuka, in a busy shipping channel.
Japanese investigators are now questioning the 20 Filipino crew members who were aboard the 728-foot long ship merchant ship.
Trump tweeted Saturday morning Washington time: "Thoughts and prayers with the sailors of USS Fitzgerald and their families". "Hopefully less than a year".
According to the website Marine Traffic, the ACX Crystal weighs 29,060 tons, while the USS Fitzgerald is 10,000 tons, CNN reported.
There was no immediate explanation for the collision.
It was unclear how the collision happened.
The bodies were taken to a USA naval hospital in Yokosuka.
Aucoin said Benson's cabin was destroyed. He is in stable condition, the Navy said.
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But it could "embolden other prosecutors to be more aggressive in their charges" since it has "such a symbolic value", he said. But a lawyer representing many of his accusers, Gloria Allred, said she was hoping the prosecution would push for a retrial.
Two other sailors were also also taken by helicopter to hospital for what the 7th Fleet said were "lacerations and bruises".
"This has been a hard day", said Vice Adm. Joseph Aucoin, commander of the U.S. Navy's 7th Fleet.
Sykes says her son told her that sailors initially believed they were under attack and some immediately went to man the guns. "Thank you to our Japanese allies for their assistance", US President Donald Trump said in a Twitter post yesterday. The ship arrived at Tokyo Bay later on Saturday.
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.
Seven sailors were reported missing when the collision happened, but not all of those missing were recovered, US Navy spokeswoman Yoko Kato said.
"Once an investigation is complete then any legal issues can be addressed", a spokesman for the USA 7th fleet told the Guardian.
The Fitzgerald and the ACX Crystal - a ship almost four times the size of the destroyer - collided early Saturday.
While photos showed serious damage above the waterline, the container ship also did severe damage below it. And as you can see now, the ship is still listing, so they had to fight the ship to keep it above the surface.
Sea and air search continues at collision site off Japan's coast between USS Fitzgerald and a merchant ship on Saturday. But such collisions at sea are rare in an age of advanced navigational technology. The weather was clear with a swell of about 1.8m at the time.
"The volume of ships is heavy in this area and there have been accidents before", Saito told Japan's public broadcaster NHK.
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