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 damage to the Fitzgerald resulted in some flooding.
The warship was towed back to Yokosuka, escorted by a Japanese coast guard ship, officials said.
The vessel was taking on water after the incident, but the crew was working to stabilize the ship by pumping water out, a US Navy official said.
The ship’s commander 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.
The Japanese coast guard said four of its vessels and one helicopter were assisting the US Navy destroyer with damage assessment and searching the area around the ship, working on the possibility that some of the missing may have fallen into the ocean.
Another US warship, the guided-missile destroyer USS Dewey, was involved in the recovery operations, US officials said.