WASHINGTON—Navy leaders have relieved the captain of a U.S. aircraft carrier after a memo to military officials in which he pleaded for help with a coronavirus outbreak at sea was leaked to a newspaper.

Capt. Brett Crozier, the commanding officer of the USS Theodore Roosevelt, now at port in Guam, was relieved Thursday after superiors said they lost confidence in his ability to lead. The decision to remove him drew outrage from lawmakers and some relatives of crew members who backed the commander’s call for attention to the crisis.

Capt. Crozier had written a four-page memorandum recently demanding that superiors allow him to take the carrier to the port in Guam to offload sailors stricken with Covid-19. At least 114 of the vessel’s crew have tested positive for the new coronavirus.

“We are not at war. Sailors do not need to die,” Capt. Crozier wrote in his March 30 memo, which was reported by the San Francisco Chronicle. “If we do not act now, we are failing to properly take care of our most trusted asset—our sailors.”

Acting Navy Secretary Thomas Modly said he made the decision to relieve Capt. Crozier because the commander’s memo left the impression that the Navy was only responding to the outbreak due to the plea.

“It creates the perception that the Navy is not on the job…and that is not true,” Mr. Modly said at a Pentagon news briefing Thursday.

He added that he expected criticism for the decision. “The responsibility for this decision rests with me,” Mr. Modly said. “I expect no congratulations.”

The decision to remove the Roosevelt commander came as a surprise to some Navy leaders, who said their focus had been getting resources to the ship, defense officials said.

Rep. Seth Moulton (D., Mass.), a former U.S. Marine and an Iraq war veteran, said the removal of the captain raised questions about Navy leadership and would draw inquiries from Congress.

“I learned on my first day in the Marines that having the courage to speak truth to power is grounds for respect, not grounds for relief,” Mr. Moulton said in a

Twitter

message.

The Navy’s decision to remove Capt. Crozier—a move tantamount to firing him from the armed services—spurred debate among top officials this week. Two of Capt. Crozier’s uniformed commanders, Adm. Mike Gilday, chief of naval operations, and Adm. John Aquilino, who is in charge of naval operations in the Pacific, questioned the decision, defense officials said.

At a Pentagon press briefing Thursday, however, Adm. Gilday said he supported Mr. Modly’s decision. Adm. Aquilino, through a spokesperson, didn’t immediately respond to a request for comment.

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Mr. Modly, a civilian official who was appointed by President Trump as undersecretary of the Navy in 2017 and became acting secretary last year, said he had no communication with the White House about the decision. He said he had relayed his decision to Defense Secretary Mark Esper.

Mr. Trump briefly addressed Capt. Crozier’s dismissal during a White House briefing on the coronavirus pandemic on Thursday, denying the move was punishment for calling attention to the plight of the crew.

“I don’t agree with that at all,” Mr. Trump said. “Not even a little bit.”

Some family members said they feared the decision to remove Capt. Crozier at the height of the crisis on the ship would slow the response, while others called it an act of retribution.

Capt. Crozier “called out the Navy, and that is why this is happening to him,” said a family member of one sailor, referring to Capt. Crozier. “He was only looking out for his sailors and this is what happens to him. It’s all about covering up for themselves.”

The post of aircraft carrier commander is among the Navy’s top jobs. Capt. Crozier is a 28-year veteran who has served as a naval aviator and officer around the world, including during the Iraq war. His removal was reported earlier Thursday by Reuters.

The Roosevelt was the first U.S. military vessel to suffer an outbreak of coronavirus while at sea. While officials don’t know how the virus came onto the ship, roughly 30 sailors had stayed at a hotel during a port visit in Vietnam earlier in March.

Initially, two sailors tested positive for the virus two weeks ago. The number has since jumped to more than 100 and is expected to keep growing, Navy officials said. The Navy last week airlifted the first several infected sailors from the aircraft carrier to medical facilities and stressed that the ship would be able to respond to any threat.

Days later, the vessel docked in Guam, where it is expected to be for weeks as sailors undergo testing and treatment.

At a news conference on Wednesday, a day before the removal, Mr. Modly had said that leaking the memo to a news organization would constitute a violation of Navy policy, and he wouldn’t rule out disciplinary action.

On Thursday, Mr. Modly said that the memo was published in Capt. Crozier’s hometown newspaper, the San Francisco Chronicle, but wouldn’t say whether he believes Capt. Crozier leaked the memo to the publication.

He said Capt. Crozier sent the memo to a “broad array of people,” resulting in it being leaked. He wouldn’t say who received copies of the memo from Capt. Crozier, only that it went to as many as 30 people.

Write to Nancy A. Youssef at nancy.youssef@wsj.com and Gordon Lubold at Gordon.Lubold@wsj.com

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