“They prevented the ship from foundering or even sinking,” Admiral Aucoin said of the crew. He declined to speculate about which ship had caused the collision.
He said he was ordering an investigation by the Navy’s Judge Advocate General, which would be led by a flag officer. In addition, he said, the United States Coast Guard would conduct its own inquiry, and the Navy would cooperate with inquiries by the Japanese authorities.
The collision occurred in a busy shipping lane south of Tokyo a little before 2:30 a.m. on Saturday, a time when most of the crew of the Fitzgerald would have been asleep. Among the compartments that flooded were cabins where 116 sailors were sleeping, Admiral Aucoin said.
About 400 vessels pass through the shipping lane each day, the Japanese Coast Guard said. Three major accidents have been reported in the area in the past five years, including at least one fatality, said Masayuki Obara, a Coast Guard official.
Mr. Obara said the Coast Guard was interviewing the crew of the Crystal to determine, among other things, whether negligent piloting by either side contributed to the collision. No injuries were reported on the Crystal, which had been traveling up the Japanese coast.
After the accident, the Fitzgerald was escorted back to its base, in Yokosuka, Japan. There and elsewhere, relatives anxiously awaited news.
“Please, we need to know more info,” a woman named Mireya Alvarez posted on the Facebook page of the Seventh Fleet on Saturday. “Two officers came to my mother’s home,” she wrote, to “tell her that my brother is one of the missing.”
The Fitzgerald’s commanding officer, Bryce Benson, was injured in the collision. He was airlifted by a Japanese Coast Guard helicopter to Yokosuka, along with two other crew members, all of whom the Navy said were conscious and under medical observation.
“His cabin was destroyed. He’s lucky to be alive,” Admiral Aucoin said of Commander Benson.
The Navy said the collision inflicted significant damage to the destroyer above and below the water line, flooding berths, a machinery area and the radio room. Photographs showed the side of the Fitzgerald caved in about one-third of the way back.
The Crystal, at 730 feet in length, is more than 200 feet longer than the Fitzgerald and, with its load of shipping containers, would weigh several times as much.
Under international maritime rules, a vessel is supposed to give way to another on its starboard side, and the damage indicates that the Crystal had been to the Fitzgerald’s starboard, and therefore had the right of way.
But maritime experts cautioned that many other factors could have led to the crash. Marine traffic records show the Crystal made a series of sharp turns about 25 minutes before the collision, which in crowded seas could cause a cascade of maneuvers by other vessels.
“Those are very high-traffic-density areas near coastal waters,” said Bill Doherty, a ship safety investigator and auditor with a long career of service on naval warships. “When a big ship like that makes a drastic change in a high traffic area, that has to be explained.”
Capt. Sean P. Tortora, a veteran merchant marine captain and consultant who said he had sailed through the area where the collision occurred, said the evidence suggested that the Fitzgerald had been at fault.
Captain Tortora described the collision as a “T-bone” in which the bow of the Crystal hit the starboard side of the Fitzgerald.
“From what I’ve seen, the Fitzgerald should have given way and passed to the stern of the container ship,” he said.
He added that a common cause of collisions, at sea or on the simulators used for training, is a misjudgment of distance and speed on the part of a captain trying to cross in front of another vessel. “They think they can make it and they make a run for it,” Captain Tortora said.
Asked about Captain Tortora’s comments, a Navy spokesman, Capt. Charles W. Brown, said it was premature to address the cause of the collision.
“At this point, our foremost concern is the search for the missing sailors and the well-being of the crew,” he said.
Another possibility, Mr. Doherty said, is that one or both vessels were acting “in extremis,” or ahead of what appears to be an imminent collision. “At that point, both vessels are burdened, and then both vessels, by law, are required to immediately take the best action to aid to avert a collision,” he said.
A former director of the National Transportation Safety Board’s office of marine safety, Marjorie Murtagh Cooke, said it could take a year or more to determine what happened.
“We don’t know what information was available to each of these vessels at the time,” Ms. Cooke said. “Was all of their equipment working? Was one vessel at anchor and the other moving? There are just so many facts that we don’t have yet.”
The Fitzgerald had recently participated in military exercises with two American aircraft carriers and ships from the Japan Maritime Self-Defense Force, as that country’s navy is known.
The ship, an Arleigh Burke class guided missile destroyer, normally carries about 300 sailors and officers. Commander Benson, 40, took the helm of the ship just a month ago.
“Thoughts and prayers with the sailors of U.S.S. Fitzgerald and their families,” President Trump wrote on Twitter on Saturday. “Thank you to our Japanese allies for their assistance.”
The Crystal, chartered by Nippon Yusen, a Japanese shipping company, had about 20 Filipino crew members on board, the company said in a statement. The cargo ship was heading toward Tokyo at the time of the collision, after making a stop on Friday at Nagoya, Japan.