The smaller guided-missile destroyer USS Fitzgerald suffered severe damage to its starboard side.
"The collision affected Fitzgerald's forward starboard side above and below the water line, causing significant damage and associated flooding to two berthing spaces, a machinery space, and the radio room," according to a statement from US 7th Fleet.
The statement hinted that the missing sailors could be trapped in the damaged area of the destroyer.
"It remains uncertain how long it will take to gain access to the spaces once the ship is pier side ... to methodically continue the search for the missing," the statement said.
The two ships collided around 1:30 a.m. local time Saturday in the Pacific Ocean, about 56 nautical miles southwest from the port of Yokosuka and 12 miles off the Izu Peninsula, the Japanese coast guard said.
The Fitzgerald had left the US naval base in Yokosuka, where it is based, earlier Friday for routine operations in the area, a US Naval Forces Japan spokesman said.
The warship was towed back to Yokosuka, escorted by a Japanese coast guard ship, naval officials said. It arrived at port late Saturday, when divers began inspecting the damage.
Earlier, the ship's commander, Cmdr. Bryce Benson, was evacuated by a Japanese naval helicopter while US military copters evacuated two injured US sailors. All three are in stable condition at the US Naval Hospital in Yokosuka, said Cmdr. Ron Flanders, public affairs officer for US Naval Forces Japan.
Five Japanese Maritime Self Defense force ships were leading the search for the missing US sailors at the site of the collision, joined by another US warship, the guided-missile destroyer USS Dewey, the 7th Fleet said. US and Japanese aircraft also were involved.
No one hurt on merchant ship
The merchant vessel involved is the ACX Crystal, a container ship flagged in the Philippines, officials said. It is chartered by Japanese shipping company Nippon Yusen Kabushiki Kaisha (NYK) and owned by Dainichi-Invest Corporation, NYK said.
No one aboard the Crystal was hurt, and no oil spilled from the vessel, NYK said.
NYK and the ship's owner are cooperating a Japan Coast Guard investigation into the collision, the shipping firm said.
"Our thoughts and deep concerns go out to all those directly affected," NYK said.
The ship-tracking website marinetraffic.com shows the ship had left the Japanese port of Nagoya on Friday evening. It was expected to dock at a Tokyo Bay port around 4:30 p.m. local time, officials said after the wreck, adding that the container ship was operating under charter to a Japanese shipping company.
Photos of the Crystal showed damage to its bow.
Shipping zone can be precarious
The area where the wreck happened is known for heavy maritime traffic, the Japanese coast guard said. About 400 to 500 ships pass through the zone each day, the service said.
The last known fatal incident there was in September 2015, when a South Korean vessel and a Japanese container ship collided, Japan's coast guard reported. Six Japanese crew were declared dead.
The area has seen two other major collisions in the past five years.
In such a busy shipping lane, the ships may have been in a "restricted navigation" situation, meaning they would have had o observe strict rules for movement and positioning in relation to other vessels in their vicinity, said Carl Schuster, former director of operations at the US Pacific Command's Joint Intelligence Center and a Hawaii Pacific University professor.
Those rules leave vessels little room to maneuver, as turning away from one ship could place a vessel at risk of an even more serious incident with another, Schuster said.
The Fitzgerald is an Arleigh Burke-class guided-missile destroyer
with a crew of approximately 330 sailors. The 10,000-ton vessel is 505 feet long.
It completed $21 million in upgrades and repairs in February and is forward-deployed to Yokosuka, supporting security and stability in the Indo-Asia-Pacific region, the service said.
The 29,000-ton container ship, which handles general cargo, includes a captain and a crew of 20, NYK said. It was built in 2008 and is about 730 feet long.
The larger size of the container ship could have left the smaller US destroyer vulnerable in the collision, Schuster said.
The force of the impact could have thrown overboard sailors who were standing on the opposite side of the destroyer from where it was struck, he said. That could account for the missing sailors, who may have been on deck on watch or even just relaxing in the night air, he said.
Sailors also could have been trapped in compartments below deck, Schuster said, pointing out that container ships have a bulbous bow below the water line, which may have plowed into the US warship.
Experienced commander in charge
Benson, the Fitzgerald's commander, was new to the position, having taken command of the vessel May 13 after serving as the ship's executive officer, or second in command, since November 2015, the Navy said last month.
The Fitzgerald is the second command for Benson, a 1999 Naval ROTC graduate of Marquette University. He commanded the minesweeper USS Guardian, operating out of Sasebo, Japan, from 2008 to 2010, before taking shore assignments in Washington and with US Pacific Command.
The collision was the second in the region for US Navy warship in just more than a month. On May 9, the guided-missile cruiser USS Lake Champlain was struck by a South Korean fishing boat
off the Korean Peninsula.
No injuries were reported in that incident, which a Navy official said occurred when the fishing boat's crew did not have a radio to hear warnings from the US warship.
The guided-missile cruiser USS Antietam ran aground
in late January while anchoring near Yokosuka, damaging its propellers and discharging 1,100 gallons of hydraulic oil into the bay.
Correction: An earlier version of this article incorrectly described the status of the commanding officer. He was transported by medevac for treatment.