WASHINGTON — President Donald Trump’s acting Navy secretary, in a profanity-laced reprimand delivered Monday, criticized sailors aboard the stricken aircraft carrier Theodore Roosevelt for cheering their captain, who was removed after he appealed for help as the coronavirus spread throughout the warship.

The Navy’s top civilian, Thomas B. Modly, delivered his message over the ship’s loudspeaker system and deepened the raw us-versus-them atmosphere that had already engulfed the carrier. It also exposed the schism between a commander-in-chief with little regard for the military’s chain of command and the uniformed Navy that is sworn to follow him.

Like much in the Trump administration, what began as a seemingly straightforward challenge — the arrival of the coronavirus onboard a nuclear-powered aircraft carrier — has now engulfed the military, leading to far-reaching questions of undue command influence and the demoralization of young men and women who promise to protect the country. At its heart, the crisis aboard the USS Theodore Roosevelt has become a window into what matters, and what does not, in an administration where remaining on the right side of a mercurial president is valued above all else.

The crew of the Roosevelt had already registered its discontent with the Trump administration’s decision to remove the commander, by cheering for Capt. Brett E. Crozier as he walked down the gangway last week and left the ship.

His letter to Navy officials pleading for help became public, prompting Modly to say he had lost confidence in Crozier for both leadership failures and for going outside the chain of command with his critique.

Modly, Navy officials say, then was angered about what he viewed as a public rebuke from the crew, and flew 8,000 miles to Guam to vent his ire to the sailors himself, according to audio recordings of the address that members of the crew shared with The New York Times and other news organizations.

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By airing his concerns in a letter through unclassified channels, Crozier showed that he was either “too naïve or too stupid to be a commanding officer of a ship like this,” Modly told the crew, some of whom said later that they were stunned by the remarks. “I understand you love the guy. It’s good that you love him. But you’re not required to love him.”

He complained that Crozier’s letter about the coronavirus on the ship caused a political headache in Guam.

“Think about that when you cheer the man off the ship who exposed you to that,” Modly said, according to the recordings. He echoed comments by the president, who on Saturday had lashed out at Crozier as well.

On Monday, Trump again criticized Crozier for writing the letter, saying it unwisely showed military weakness. But he also said he had heard good things about the carrier’s former commander.

“His career prior to that was very good,” Trump said. “So I’m going to get involved and see exactly what’s going on there because I don’t want to destroy somebody for having a bad day.”

In the close-knit world of the American military, the crisis aboard the Roosevelt — known widely as the “T.R.”— generated widespread criticism from men and women who are usually careful to steer clear of publicly rebuking their peers.

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Modly’s decision to remove Crozier without first conducting an investigation went contrary to the wishes of both the Navy’s top admiral, Michael M. Gilday, the chief of naval operations, and the military’s top officer, Gen. Mark A. Milley, the chairman of the Joint Chiefs of Staff.

“I am appalled at the content of his address to the crew,” retired Adm. Mike Mullen, the chairman of the Joint Chiefs of Staff under Presidents George W. Bush and Barack Obama, said in a telephone interview, referring to Modly.

Modly, Mullen said, “has become a vehicle for the president. He basically has completely undermined, throughout the T.R. situation, the uniformed leadership of the Navy and the military leadership in general.”

The Trump administration’s handling of the crisis aboard the Roosevelt reflects a growing divide between senior uniformed commanders and their civilian bosses.

“At its core, this is about an aircraft carrier skipper who sees an imminent threat and is forced to make a decision that risks his career in the act of what he believes to be the safety of the near 5,000 members of his crew,” said Sean O’Keefe, a former Navy secretary under President George H.W. Bush. “That is more than enough to justify the Navy leadership rendering the benefit of the doubt to the deployed commander.”

In the days after Crozier’s letter for help was made public, Gilday, the Navy chief, argued that, per usual Navy procedures, an investigation into what went wrong on the Roosevelt should be allowed to play out. But Modly overruled him, saying Crozier had cracked under pressure.

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Defense Secretary Mark T. Esper said Sunday that he supported Modly’s decision. Milley, for his part, told Fox News, “I trust Secretary Modly in his judgment, and I am going to support him.”

Several current and former Navy and national security officials said the Roosevelt episode illustrated how civilian leaders in this administration made questionable decisions based on what they feared Trump’s response would be.

“Modly got involved in the day-to-day deliberations to a greater degree than Navy tradition and the chain of command would expect precisely because Modly was obsessed with how the story might be playing inside the White House,” said Peter D. Feaver, a political-science professor at Duke University who has studied military-civilian relations.

The Roosevelt issue is the second in just five months in which the views of Trump and his political appointees have precipitated a crisis in the uniformed Navy. Modly, a Naval Academy graduate and former helicopter pilot, would not be in his current acting position were it not for the last political imbroglio, which involved the firing of the previous Navy secretary, Richard Spencer, by Esper in November.

Spencer had publicly disagreed with Trump’s intervention in an extraordinary war crimes case involving a member of the Navy SEALs, Chief Petty Officer Edward Gallagher, who was accused of murdering a wounded captive with a hunting knife during a deployment to Iraq in 2017.

Gallagher had caught the president’s eye. Trump saw the commando as a victim of political correctness that he said hamstrings the warriors the nation asks to defend it.

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When the Navy prosecuted Gallagher, Trump intervened several times in his favor. When the chief’s court-martial ended in acquittal on most charges, Trump congratulated him and criticized the prosecutors. After the Navy demoted Gallagher for the one relatively minor charge on which he was convicted, Trump reversed the demotion.

Finally, the commander of Naval Special Warfare, Rear Adm. Collin P. Green, started the formal process of taking away Gallagher’s Trident pin, symbol of the Navy commandos, and expelling him from the SEALs. But Trump overruled the move — and Esper fired Spencer, who had supported the process of taking away Gallagher’s Navy SEAL pin.

“The Navy will NOT be taking away Warfighter and Navy Seal Eddie Gallagher’s Trident Pin,” Trump wrote on Twitter in November. “This case was handled very badly from the beginning. Get back to business!”

The coronavirus hit the Roosevelt as Trump was seeking to project a confident message of the United States getting through the pandemic with relative ease.

The acting Navy secretary “knew the president had sacked his predecessor when an internal matter of military discipline became the fodder for Fox News morning shows, and so was keen to manage — some would say, micromanage — the political optics,” Feaver said.

Modly arrived aboard the Roosevelt around 1 p.m. Guam time Monday with little warning. Eight bells signaled his arrival, and he quickly made his way to one of the hangar bays, where he addressed thousands of the ship’s crew over the public address system.

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Though some of the crew from the Roosevelt are quarantined in hotels in Guam, many were still aboard when Modly arrived.

When the network of small talk boxes wired across the cavernous network of passageways — common on a 1,000-foot nuclear-powered aircraft carrier — clicked on, crew members craned their necks to listen. Someone important was talking.

“I’ve been wanting to come out to the ship since we first found out you had COVID cases on here,” Modly began. He talked about how China was responsible for the virus, and accused the Beijing government of worsening the crisis by failing to disclose how bad it was. And he went into his message, which alternated between criticizing Crozier and admonishing the crew.

When his 15-minute speech was over, signing off with a tepid “Go Navy,” Modly had effectively drawn an invisible line between him and the more than 4,800 crew members of the Roosevelt, one crew member said. This sailor added that many of the crew thought Modly had called them stupid for putting so much faith in their commanding officer. After Modly’s speech, junior sailors approached the crew member, he said, looking to leave the service after their first enlistment.

Modly did not tour the ship, and practically no one, especially those in the lower ranks, even saw him. He was gone in less than 30 minutes.

Some crew members said they thought Modly’s tone derived from the questions submitted by the crew before his arrival. Even though the questions were screened for professionalism and appropriateness, crew members said, many of them centered on Crozier’s firing.

In the end, the questions may not have mattered anyway. Modly did not answer a single one.