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“As we have seen with the vaccine mandates, these court decisions are subject to review on appeal,” Jason Abrams, an Amtrak spokesman, said in a statement.

Many public transit agencies across the country also appeared to be keeping their mask mandates in place in the hours after the ruling. Those include the Metropolitan Transportation Authority in New York City; New Jersey Transit; the Metro and bus system in Washington, D.C.; the Massachusetts Bay Transportation Authority in Boston; the Southeastern Pennsylvania Transportation Authority in Philadelphia; and the Chicago Transit Authority.

President Trump appointed Judge Mizelle to the bench in November 2020, after he had lost re-election. A former clerk to Justice Clarence Thomas, she was 33 years old at the time, making her the youngest person Mr. Trump appointed to a life-tenured judgeship; the American Bar Association declared her not qualified because of her lack of experience, but Republican senators confirmed her in a party-line vote.

Lawrence Gostin, a professor of global health law at Georgetown University, said that the Biden administration would have to appeal the decision if it wanted the mandate to continue. He also defended the agency’s authority to issue the mask requirement.

“If there were ever an instance where the C.D.C. has authority to act, the classic case is to prevent the interstate transmission of a dangerous infectious disease,” he said.

Apart from the legal issues concerning the scope of the C.D.C.’s authority to protect public health, as a matter of policy, Judge Mizelle’s ruling was greeted by some in the airline industry as a relief.

David Neeleman, who has founded several airlines including JetBlue Airways and Breeze Airways, which started flying last year, said he welcomed the end of a mask mandate for passengers. Crew members at Breeze, where Mr. Neeleman is the chief executive, have been frustrated by having to police passengers, creating unnecessary tension in flight, he said.