"... You will see the USS Fitzgerald back as one of our warships here, but it will require some time".
Vice Adm. Richard P. Breckenridge called the crash a "tragedy" that should remind Americans of the danger US sailors face every day.
The Navy's 7th Fleet said the bodies were found on Sunday morning after the ship returned to its base in Japan.
"There wasn't a lot of time in spaces that were open to the sea".
Aucoin said that much of the crew of about 300 was asleep when the collision happened at 2:20 a.m. Saturday, and that one machinery room and two berthing areas for 116 crew members were severely damaged. "I am humbled by the bravery and tenacity of the Fitzgerald crew".
Benson was flown off the crippled ship by helicopter after the accident and was being treated at the naval hospital at Yokosuka, according to Aucoin, as were two other sailors who were medevaced.
Aucoin said, that this has been a hard day, adding that the search for missing shipmates would continue now that the vessel was back in Yokosuka.
Fitzgerald's commander, Cmdr. Bryce Benson, was evacuated by a Japanese naval helicopter while U.S. military copters evacuated two injured United States sailors.
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The destroyer collided with the container ship - four times the size of the naval vessel - about 104km south-west of military port city Yokosuka.
NYK and the ship's owner are cooperating with a Japan Coast Guard investigation into the collision, the shipping firm said.
The seven sailors didn't make it out of the berthing area, the Navy said.
Seven sailors were previously reported missing, although officials have not yet said how many bodies were recovered from the USS Fitzgerald.
US President Donald Trump tweeted, "Thoughts and prayers with the sailors of USS Fitzgerald and their families".
He thanked "our Japanese allies" for their swift assistance, and said the Navy will full investigate the cause.
Aucoin wouldn't speculate on the cause of the collision in an area busy with sea traffic.
"Our government expresses its heartfelt solidarity with the United States at this hard time, and will spare no effort in supplying any and all assistance", Japan's prime minister Shinzo Abe said on Sunday.
The ACX Crystal, 222.6 metres long and weighing 29,060 tons, sailed to Tokyo with superficial damage.
The coast guard questioned crew members of the ACX Crystal, and is treating the collision as a case of possible professional negligence, said Masayuki Obara, a regional coast guard official.
"Just heard the sweetest voice and saw a wonderful face".
Mia Sykes of Raleigh, North Carolina, told The Associated Press on Sunday that her 19-year-old son Brayden Harden was knocked out of his bunk by the impact, and water immediately began filling the berth.
In a statement released earlier on Facebook, US chief of naval operations Admiral John Richardson said new information will be released as they receive it.