Planes, boats and helicopters scoured the seas off Japan's Pacific coast in a bid to find the crew who disappeared in the predawn accident, which also left the USS Fitzgerald's skipper injured.
It was not clear where the missing sailors were when the collision happened.
Several other crew members were injured and had to be evacuated by air to hospital, including the guided missile destroyer's commanding officer Bryce Benson.
Aerial television footage showed one person lying on a stretcher and a rescuer being pulled up to a helicopter that was hovering above the Fitzgerald, part of its right side caved in.
"There are seven sailors unaccounted for; the ship and the Japanese Coast Guard continues to search for them," the Navy said.
The collision between the Fitzgerald and Philippine-flagged container ship ACX Crystal happened around 2:30 am (1730 GMT Friday) off the coast of the Izu peninsula, southwest of Tokyo.
The area is a busy shipping channel that is a gateway to major container ports in Yokohama and Tokyo.
"The volume of ships is heavy in this area and there have been accidents before," coastguard official Yutaka Saito told Japan's public broadcaster NHK.
NHK said the massive 222-metre (730 foot) container ship made a sharp turn around the time of the accident, but its captain suggested otherwise.
"(We) were sailing in the same direction as the US destroyer was and then collided," he was quoted as saying by Jiji Press news agency.
'Going all out'
Japan's coastguard, which is probing the incident, said it has sent a half dozen vessels, several aircraft and a team of specially-trained rescue personnel to the scene. They were later joined by the country's Self-Defence Forces.
"We're going all out in the search to find these missing people... but we still haven't found any clues about where they might be," a coastguard spokesman said, adding that the search may continue overnight.
The 154-metre Fitzgerald -- which was commissioned in 1995 and deployed in the Iraq war in 2003 -- is based in Yokosuka, operating in the Pacific and the Sea of Japan (East Sea).
"My daughter is on the Fitzgerald," a parent wrote on the 7th Fleet's Facebook page.
"So worried. Just need to hear she is ok. Thinking of all of our sailors and their families!!"
US chief of naval operations Admiral John Richardson said in a statement: "As more information is learned we will be sure to share it with the Fitzgerald families and when appropriate the public.
"All of our thoughts and concerns are with the Fitzgerald crew and their families."
Television images showed heavy damage to the right side of the Fitzgerald just ahead of the control tower, and that the ship had taken on water.
"The USS Fitzgerald suffered damage on her starboard side above and below the waterline. The collision resulted in some flooding," the Navy said.
The navy said that while "her propulsion was limited", the ship was not in danger of sinking and it headed back to port under its own power.
The ACX Crystal, meanwhile, appeared to have relatively minor frontal damage, and none of its 20 crew were injured, the coastguard said.
The vessel -- which was sailing to a Tokyo port today afternoon -- is a commercial container ship with a Filipino crew, according to its Japanese owner, NYK Line.
It had left the central Japanese city of Nagoya on Friday and was due to arrive in the capital today.
"We can't comment on the accident as it's being handled by the Japanese coastguard," a company spokesman told AFP.
"We will fully cooperate with authorities investigating the case."