President Donald Trump retweeted an update Saturday from the USA 7th Fleet on the ship's status and the search-and-rescue mission, saying: "Thoughts and prayers with the sailors of USS Fitzgerald and their families. Thank you to our Japanese allies for their assistance", Trump tweeted.
The collision happened at about 2:30 a.m. local time (1730 GMT), some 56 nautical miles southwest of Yokosuka, the Navy said.
The U.S. Navy says one of its destroyers, the USS Fitzgerald, collided with a Philippine-flagged merchant vessel off the coast of Japan.
The vessel was taking on water after the incident, but the crew was working to stabilize the ship by pumping water out of the hold, a US Navy official told CNN.
The USS Fitzgerald, flanked by two tug boats and other support vessels, was listing to its right as it slowly approached Yokosuka Naval Base, south of Tokyo.
The Arleigh Burke-class guided-missile destroyer USS Fitzgerald conducts tactical maneuvers with a ship from the Republic of Korea navy in March of 2013.
Numerous details of the nighttime collision remain unknown. Three, including the captain, have been injured.
Nippon Yusen said all of the ACX Crystal's 20-member Filipino crew members were safe.
At around 29,000 tons displacement, the ship dwarfs the 8,315-ton US warship, and was carrying 1,080 containers from the port of Nagoya to Tokyo.
Two other crew members suffered cuts and bruises and were evacuated, it said.
While the cause of the collision remains unclear, Japan's public broadcaster NHK said the ACX Crystal had made a sharp turn shortly before the collision.
Five Japanese Maritime Self Defense force ships were leading the search for the missing United States sailors at the site of the collision, joined by another USA warship, the guided-missile destroyer USS Dewey, the 7th Fleet said.
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The Navy's 7th Fleet reported the developments in an update on the stricken ship that was nearing the port of Yokosuka in Japan. "[It resulted in] some flooding", it said.
At the time of the collision, most of the crew were probably asleep.
It was not clear where the missing sailors - still unaccounted for some 20 hours later - were when the huge vessels collided and the search was expected to continue overnight.
Her grandson Jackson Schrimsher is a 23-year-old sailor aboard the USS Fitzgerald.
"Of course we're nervous and scared and just praying", Rita Schrimsher said by telephone from Athens, Alabama. Seven sailors, however, were missing following the collision. Japan's coast guard says they were thought to have been thrown into the sea or possibly trapped inside damaged sections of the destroyer.
Three people injured in the incident have been moved to the U.S. Naval Hospital in Yokosuka.
The Navy said in a statement that Cmdr.
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.
It is chartered by Japanese shipping company Nippon Yusen Kabushiki Kaisha (NYK) and owned by Dainichi-Invest Corporation, NYK said.
This item clarifies that Richardson is the head of Navy.
The US Navy was still working to determine the number and extent of injuries Saturday morning, but reported that one sailor was being evacuated via Japanese Coast Guard helicopter.
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