"Right now we are focused on two things: the safety of the ship and the well-being of the Sailors", Adm. Scott Swift, commander of the U.S. Pacific Fleet, said in a statement.
The ship, with a capacity of 29,060 tons, was travelling from Nagoya Port to Tokyo Port, and carrying 1,080 containers.
Several personnel were also injured in the incident which happened early on Saturday morning.
Footage from the Japanese TV network NHK showed heavy damage to the middle right side of the Navy ship and a person in a stretcher being lifted to a helicopter.
The Japanese Coast Guard was searching for the missing and the USS Dewey and two navy tugs were also dispatched to provide help, as well as helicopters and other aircraft.
Vice Adm. Joseph P. Aucoin, commander of US 7th Fleet, along with many family members, were present when the ship arrived, reports the Navy.
Despite efforts to ease the intake of water, the statement said it was "uncertain how long it will take to gain access to the spaces once the ship is pier side in Yokosuka".
The nighttime collision off Japan left seven U.S. Navy sailors from USS Fitzgerald missing.
The cause of the collision wasn't immediately clear.More news: Russian Federation set for World Cup stress test in Confed Cup
The American ship, the Arleigh Burke-class guided-missile destroyer USS Fitzgerald, was built at Bath Iron Works in ME and commissioned in 1995.
DESTROYER DESTROYED Damage is seen on the guided missile destroyer USS Fitzgerald off the Shimoda coast, after it collided with a Philippine-flagged container ship.
The incident at about 2.30am local time (1.30am in Singapore) left at least three sailors injured, including the United States ship's captain, Commander Bryce Benson, who suffered a head injury and was evacuated by helicopter. He suffered an injury to the head, according to Fox News.
The Philippine government on Saturday said it was ready to assist Filipino seafarers aboard the ACX Crystal vessel that collided with the US Navy destroyer, although the Department of Foreign Affairs (DFA) later said no Filipino was injured in the accident.
Twenty crew members were aboard the container and none was injured, a Japanese coast guard spokesman confirmed, adding that the vessel was sailing back to a Tokyo port.
The U.S. 7th Fleet said on its Facebook page that the collision was with Philippine-flagged merchant vessel ACX Crystal.
The US and Japan were conducting a major search operation yesterday to find seven missing American sailors. "The collision resulted in some flooding", the US Navy said. Officials said shortly after 2 p.m. Saturday Tokyo time that flooding had been stabilized. People were standing on various parts of the deck. A US defense official said there is flooding in three compartments of the Fitzgerald. A USA defense official said there is flooding in three compartments of the Fitzgerald, and there were injuries. The Japanese Coastguard told CNN that the U.S. destroyer and the merchant ship collided off the coast of Japan in the Pacific Ocean.
Three aboard the destroyer had been medically evacuated, including the ship's commanding officer, Cmdr Bryce Benson, who was reportedly in stable condition after being airlifted to the US Naval Hospital in Yokosuka.
The Pacific Fleet said the extent of injuries and damage to the Fitzgerald are "being determined", and the incident is under investigation.