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.
Tugboats pulled the Fitzgerald back to port in Yokosuka in southern Japan yesterday, 16 hours after the Philippine-flagged merchant ship ACX Crystal collided with the destroyer 56 miles out at sea.
As search and rescue crews gained access to the spaces that were damaged during the collision this morning, the missing Sailors were located in the flooded berthing compartments.
The captain, Commander Bryce Benson, suffered a head injury and was airlifted to shore, and Mr Aucoin said he is lucky to have survived.
"The families are being notified and being provided the support they need during this hard time", the Seventh Fleet said.
Vice Adm. Joseph Aucoin wouldn't say how many bodies were found but said the identities of the sailors would be released following notification of the families.
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The crash happened at 2.30am Saturday local time, around 56 miles southwest of the city of Yokosuka, which is home to a United States naval base.
The other two were being treated for lacerations and bruises and others injured were being assessed aboard the ship.
Water rushed into the ship as the impact crushed the Fitzgerald's forward starboard side, above and below the waterline, damaging two berthing spaces, a machinery area and the ship's radio room, the Navy said. "Now that the ship is in Yokosuka, I ask that you help the families by maintaining their privacy as we continue the search for our shipmates".
The Japanese coast guard said it received an emergency call from the container ship, the ACX Crystal, reporting the collision around 2:20 a.m. local time. He said he would order a full and thorough investigation.
While photos showed serious damage above the waterline, the container ship also did severe damage below it.
The bodies were found in previously flooded compartments, including sleeping quarters. The container ship's left bow was dented and scraped, but it did not appear to have sustained any major structural damage.
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At 29,060 tonnes, the container ship was more than three times as big as the Navy destroyer.
Nippon Yusen KK, which chartered the merchant vessel, said it would "cooperate fully" with the investigation into the crash.
The 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.
"I express my heartfelt solidarity to America at this hard time", he said, praising USA servicemen in Japan under the allies' bilateral security pact.
"Just heard the sweetest voice and saw a wonderful face".
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