WASHINGTON — The acting secretary of the Navy on Wednesday ordered a wider investigation into events aboard the aircraft carrier USS Theodore Roosevelt, shelving for now a recommendation by the Navy’s top admiral to restore Capt. Brett E. Crozier to command the virus-stricken warship.

“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.

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 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 USS Theodore Roosevelt,” McPherson said.

His announcement came just days after Gilday recommended giving Crozier his job back. But 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.

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The decision essentially kicks down the road any action on Gilday’s recommendation that 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 Donald Trump. Crozier was fired in part because of fears that 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 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.

A two-paragraph statement by McPherson, formerly the Navy’s top military lawyer, made no mention of Crozier’s fate. A spokeswoman for McPherson said that Capt. Carlos Sardiello, a former commanding officer of the Roosevelt who was summoned back after 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 likely take about 30 days.

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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,” Rep. Adam Smith, D-Wash., who heads the House Armed Services Committee, told reporters on a conference call.

But, Smith added, “I personally think that Capt. Crozier should be reinstated.”

Sen. 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 Capt. 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, Crozier has assumed the role of an unlikely hero, willing to sacrifice a three-decade career for the sake of his sailors.

After Crozier was fired by the acting Navy secretary at the time, his personal setback took on momentum as a larger cause. Videos of hundreds of sailors cheering their skipper as he walked off the ship’s gangway went viral on social media.

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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. Modly resigned.

Milley had agreed with Gilday, the Navy’s top officer, in advising that Crozier not be removed until an investigation into the events aboard the Roosevelt was complete. But Modly waved off those warnings, fearing that Trump wanted Crozier fired, according to his acquaintances, and dismissed the skipper.

Trump’s position appeared to ease, however, given the support for Crozier in the Navy and among the general public. The president has not made clear where he stands on Crozier’s reinstatement, leading some Pentagon officials to conclude that 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 USS Kidd, the second deployed U.S. 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.