Seven crew members from the U.S. Navy's guided-missile destroyer USS Fitzgerald remained unaccounted for and three others were injured following a collision between the destroyer and a Philippine container vessel in waters off Shizuoka Prefecture, in the southeast part of central Japan, early Saturday morning.
Officials are now questioning the freighter's crew at Tokyo's Oi wharf over the cause of the night-time crash.
Three sailors required medical evacuation from the damaged Fitzgerald, according to a release.
Family members are frantically seeking news, appealing via social media for sailors aboard the ship to get in touch.
A spokesman for the United States 7th Fleet said the ship was heading back to Yokosuka under its own power at 3 knots.
Most of the more than 200 sailors aboard would have been asleep in their berths at the time.
Vice Admiral Joseph P Aucoin, the commander of the 7th Fleet, said: "This has been a hard day".
The Pentagon confirms search efforts are underway for the Fitzgerald's seven missing crew members, with help from the Japanese coast guard. The Fitzgerald is deployed to Yokosuka, supporting security and stability in the Indo-Asia-Pacific region, where tensions between the U.S and North Korea have led to fears over the possibility of World War 3 beginning in the area.
The USS Fitzgerald's captain, Commander Bryce Benson, was airlifted to the US Naval Hospital in Yokosuka after the collision and is in stable condition with a head injury, the Navy said.
The Japan Coast Guard has confirmed that seven crew members are missing and one is injured. It is unclear how many others may have been hurt.
Under worldwide regulations on preventing collisions at sea, when two vessels are in a crossing situation, a ship must give way to the vessel to starboard.
The ACX Crystal, a 222-metre (730ft) Filipino-flagged container ship, was travelling between the Japanese cities of Nagoya and Tokyo.
The coast guard is investigating the accident with the U.S. Navy and questioned the crew members of the 29,060-ton ACX Crystal, operated by Japanese shipping firm Nippon Yusen K.K., with an eye on possible endangerment of traffic caused by professional negligence.
The accident happened 56 nautical miles (104 kilometers) southwest of the base, the US Navy said.
The Navy ship's starboard side was heavily damaged in the collision, but the vessel later managed to slowly return to its base in Yokosuka, with the assistance of U.S. navy tug boats. Their names are being withheld until the families have been notified, it added.
"We're going all out in the search to find these missing people... but we still haven't found any clues as to where they might be", a coastguard spokesman said.
"So anxious. Just need to hear she is OK. He's okay. Thank you all for the prayers", tweeted Rita Schrimsher of Athens, Alabama, after speaking with her 23-year-old grandson, Jackson Schrimsher, via Facetime. She says: "It could have been worse so we're grateful".