“I have unanswered questions that the preliminary inquiry has identified and that can only be answered by a deeper review,” the acting secretary, James E. McPherson, said in a statement.
Mr. McPherson said he was directing the chief of naval operations, Adm. Michael M. Gilday, to investigate, expanding a preliminary review that the Navy completed and presented to Defense Secretary Mark T. Esper last week.
“This investigation will build on the good work of the initial inquiry to provide a more fulsome understanding of the sequence of events, actions and decisions of the chain of command surrounding the Covid-19 outbreak aboard U.S.S. Theodore Roosevelt,” Mr. McPherson said.
His announcement came just days after Admiral Gilday recommended giving Captain Crozier his job back. But Mr. Esper, who initially said he would leave the process largely with the military chain of command, declined to endorse the findings last week, saying that he wanted to review the Navy’s investigation into the matter first.
Gen. Mark A. Milley, the chairman of the Joint Chiefs of Staff, had also told associates that he favored a wider inquiry into the Roosevelt matter.
The decision essentially kicks down the road any action on Admiral Gilday’s recommendation that Captain Crozier be reinstated, and was seen by some people within the Defense Department as reflecting concern among both civilian and military officials at the Pentagon over getting on the wrong side of President Trump. Captain Crozier was fired in part because of fears that Mr. Trump wanted him gone, and not knowing how the president feels about reinstating the captain has cast a shadow over the actions since.
“More and more, this looks like the military leadership and civilian leadership having very divergent goals,” said Jon Soltz, an Iraq war veteran who is the chairman of VoteVets.org. “The military seems to not be interested in punishing a captain for taking desperate action to save the lives of his crew members.”
But the Defense Department’s civilian leadership, he said, “seems more interested in protecting the Trump administration’s image, even if that means hanging commanders out to dry.”
Reinstating Captain Crozier could be a remarkable reversal to a story that has seized the attention of the Navy, the military and even a nation struggling with the coronavirus. Instead, it is unclear who will be at the helm of the nuclear-powered carrier as its 4,800-member crew prepares to leave its weekslong quarantine in Guam to resume operations in the western Pacific.
Mr. McPherson’s two-paragraph statement made no mention of Captain Crozier’s fate. A spokeswoman for Mr. McPherson said that Capt. Carlos Sardiello, a former commanding officer of the Roosevelt who was summoned back after Captain Crozier was dismissed, would remain in charge for now.
Navy officials said the broader investigation would be conducted by an admiral outside the Pacific region and would most likely take about 30 days.
Senior lawmakers reacted with some skepticism to the Navy’s latest decision.
“It’s perfectly legitimate to extend the investigation about everything that happened with the Roosevelt,” Representative Adam Smith, a Washington Democrat who heads the House Armed Services Committee, told reporters on a conference call.
But, Mr. Smith added, “I personally think that Captain Crozier should be reinstated.”
Senator Jack Reed of Rhode Island, the senior Democrat on the Senate Armed Services Committee, said in a statement, “This investigation should be thorough and expeditious.” He added, “The removal of Captain Crozier was highly unorthodox and the recommendations of the military leadership on his reinstatement should be heavily weighed.”
From the moment his letter pleading for assistance from top Navy officials became public, Captain Crozier has assumed the role of an unlikely hero, willing to sacrifice a three-decade career for the sake of his sailors.
An ill-fated trip to the carrier afterward by the acting secretary, Thomas B. Modly, backfired when he criticized the crew for supporting its deposed captain. Mr. Modly resigned.
General Milley had agreed with Admiral Gilday, the Navy’s top officer, in advising that Captain Crozier not be removed until an investigation into the events aboard the Roosevelt was complete. But Mr. Modly waved off those warnings, fearing that Mr. Trump wanted Captain Crozier fired, according to his acquaintances, and dismissed the skipper.
Mr. Trump’s position appeared to ease, however, given the support for Captain Crozier in the Navy and among the general public. The president has not made clear where he stands on Captain Crozier’s reinstatement, leading some Pentagon officials to conclude that Mr. Esper’s hesitation in accepting the Navy’s recommendations would allow time to account for the views of the president.
The announcement on Wednesday comes as the crew of the Roosevelt begins its long-scheduled turnover: swapping out those sailors who remained behind to clean the ship with healthy crew members who were isolated on Guam for the past several weeks.
In the coming days, the Roosevelt will start a series of sea trials, requalifying flight crews and pilots, before carrying on with its deployment in the western Pacific.
This week, the Kidd, the second deployed American warship stricken with the virus, returned to port in San Diego with at least 64 members of its crew testing positive for the illness, according to a Navy news release. The Kidd, a destroyer, was previously operating in the eastern Pacific and the Caribbean as part of a counternarcotics operation.
Thomas Gibbons-Neff contributed reporting.