Several Japanese and US boats and aircraft have been deployed, with the search continuing into the night.
An investigation into how the USS Fitzgerald collided with a Philippine-registered container ship in the early hours of Saturday morning has begun.
The ship’s commanding officer was among three people aboard to be hospitalised.
The incident took place some 56 nautical miles (104km) south-west of the Japanese port city of Yokosuka, at about 02:30 local time on Saturday (17:30 GMT Friday).
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 US navy tug boats.
The collision occurred near Yokosuka, which is home to the US 7th Fleet that comprises up to 80 submarines and ships, including the USS Fitzgerald.
It is unclear where the 154-metre (505ft) guided missile destroyer ship was heading at the time.
The ACX Crystal, a 222-metre (730ft) Filipino-flagged container ship, was travelling between the Japanese cities of Nagoya and Tokyo.
Marine traffic records suggest the ACX Crystal made a sudden U-turn roughly 25 minutes before the collision with the USS Fitzgerald. It is not clear why it changed course.
Marine traffic records suggest it was travelling at 14.6 knots (27km/h) at the time of the collision.
Japan’s coastguard is co-ordinating the search with US teams for the seven missing crew members, who have not yet been publicly identified. It has sent half a dozen vessels, a number of aircraft and rescue personnel to the scene.
It is not yet known where the missing sailors were when the collision happened.
The US navy says several compartments were severely damaged – including the ships radio room, and two berthing compartments, the BBC’s Rupert Wingfield-Hayes reports from Tokyo.
Some of the seven missing sailors may have been asleep in those compartments when the collision happened.