Some large U.S. transit systems are keeping mask mandates in place, for now.

Masks in the skies? Largely no more. But on trains, buses and even ferries across America on Tuesday, many passengers were told to keep them on.

As major U.S. airlines dropped their mask mandates in response to a federal judge’s ruling, public transit systems across the country scrambled to adapt. New York, Chicago, Seattle and San Francisco all kept requirements in place, while systems in New Jersey, Atlanta, Washington and Philadelphia allowed riders to drop their masks, as did the nationwide Amtrak rail system.

In Philadelphia, the decision led to an odd juxtaposition: The city last week reinstated its mask mandate for indoor public spaces, becoming the first major U.S. city to do so this spring. But a statement late Monday announced an end to the requirement on city trains and buses, and in stations and concourses.

Officials with the Southeastern Pennsylvania Transportation Authority, or SEPTA, wrestled with a response to the judge’s ruling. “It was a bit of a scramble,” said Andrew Busch, the Philadelphia agency’s spokesman. The overriding concern was that keeping the mask requirement would create challenges for employees charged with enforcing it, who have already faced pushback and harassment.

“We wanted to try to reassure our employees that they wouldn’t be in a difficult position of trying to figure out how to tell people that this was required, when the mechanism for requiring it was no longer in place,” Mr. Busch said.

In Boston, less than a day after the local transit agency said masks were still required on subways and buses, officials on Tuesday afternoon announced a reversal. Mask mandates were also lifted at Boston Logan International Airport and at most regional transit authorities across Massachusetts.

Chicago’s commuter rail system, Metra, originally said it was taking the issue day by day. After the Illinois governor amended a state mask mandate on Tuesday, it quickly announced that “masks would be welcome but not required.” For now, train, bus and subway riders in Chicago are still required to wear masks.

Even in places where masks will continue to be required, officials — many of them along the West Coast — acknowledged that it might only be a matter of time.

“There may be an appeal from the Justice Department that could lead to a delay in implementation, or for the decision to be altered or overruled,” Seattle’s King County Metro said on Monday. “In the meantime, Metro’s mask mandate remains in effect.”

Portland’s TriMet agency and the operator of San Francisco’s city bus system, the San Francisco Municipal Transportation Agency, made similar announcements.

The patchwork of responses underscored the uncertainty of the current phase of the pandemic. The Omicron subvariant known as BA.2 has reversed a nationwide decline in new cases — a trend that can be seen even with diminishing test data. But the virus is spreading in a country that is better vaccinated than during previous surges, and so far, an increase in hospitalizations has not followed the rise in infections.

Even in places that have kept mask requirements, enforcement has long been virtually nonexistent on trains and buses. In Atlanta, where a mandate was in place until Tuesday, Aida Smith, 22, said that she had stopped masking on public transit after she was vaccinated against the coronavirus last year.

“I feel like a lot of other people here did the same thing — got vaccinated and stopped wearing a mask,” she said.

Darren Kettle, the chief executive of Metrolink, a commuter rail system that serves six large Southern California counties, said that officials spent most of the day on Monday figuring out what exactly the federal court ruling meant.

But once he got word that the Transportation Security Administration would be lifting its mask requirement, he said, Metrolink decided to follow suit. “Not having this in place now gives people peace of mind that at least our conductors aren’t having to enforce something that was very difficult to enforce,” he said.