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Amy Thibault, a spokeswoman for CVS, cited “the current regulatory environment” as the reason the vaccine was not available in those states, or in the District of Columbia, emphasizing that the list could change. Legal experts said that federal decisions were creating an extremely difficult situation for pharmacies to navigate.

In some states, pharmacists are forbidden to administer vaccines that are not recommended by the Advisory Committee on Immunization Practices, a Centers for Disease Control and Prevention panel.

Last year, the panel voted to recommend updated Covid vaccines in June. In 2023, it endorsed new Covid vaccines in September, just one day after the F.D.A. gave its approval.

But as of this Thursday, the panel was not scheduled to meet for another three weeks. And, after a slew of high-level resignations at the C.D.C., Senator Bill Cassidy — Republican of Louisiana and the chairman of the Senate’s health committee — has called for the meeting to be “indefinitely” postponed. That could mean many people’s access to shots remains hamstrung well into the fall, when infections from respiratory viruses normally spike.

CVS will make the vaccines available nationwide if the advisory panel recommends them, Ms. Thibault said. But since the panel hasn’t yet made a decision, the company is holding off in states where it believes its pharmacists need a C.D.C. endorsement.

Those states are Arizona, Colorado, Florida, Georgia, Kentucky, Louisiana, Maine, Massachusetts, Nevada, New Mexico, New York, North Carolina, Pennsylvania, Utah, Virginia and West Virginia, along with the District of Columbia. Pharmacies have traditionally been a crucial access route to the Covid vaccine, accounting for a vast majority of shots given last year. The CVS move is a strong signal that federal decisions could reduce access more than the restrictions laid out on paper, and the confusion is likely to crop up at other pharmacies as well, legal experts said. Walgreens, the nation’s second largest pharmacy chain, did not respond to requests for comment about the availability of Covid shots at its stores. But when a New York Times reporter tried to schedule vaccine appointments in all 50 states, the pharmacy’s website said patients would need a prescription in 16.

Requiring prescriptions for the shots would be a total change in practice, said Dr. Marc Sala, a co-director of the Northwestern Medicine Comprehensive Covid-19 Center in Chicago. Experts are themselves divided on what pharmacies can do, but they agree that the choices are hard.

Whether last year’s C.D.C. recommendation still applies is ambiguous, said Richard Hughes IV, a vaccine lawyer who teaches at George Washington University Law School and worked for Moderna early in the pandemic. There is an argument that it does, and that pharmacists can administer the updated vaccines under it unless ACIP says otherwise, he said.

But Richard Dang, an associate professor of clinical pharmacy at the University of Southern California, said he believed the reformulated shots required a new recommendation.

In the states where Walgreens is requiring prescriptions, it appears to have judged that its pharmacists can perform the actual injections, but can’t determine the appropriateness of a vaccine for a particular patient. Those questions are legally separate, Mr. Hughes said.

Vaccine appointments also appeared unavailable at Walgreens in many states. That may, in part, reflect a supply issue, doctors said. But Walgreens’ note that patients need prescriptions in some states could signal confusion among pharmacists over whom they’re allowed to vaccinate.

“That may be pharmacies covering themselves while all of these unanswered questions are still up in the air,” said Dr. Shira Doron, the chief infection control officer for Tufts Medicine.

Covid vaccination rates have fallen precipitously since the height of the pandemic. Just 23 percent of adults and 13 percent of children reported getting an updated Covid vaccine last season. The fact that pharmacies are limiting access to vaccines when Covid infections are rising, as they do every summer, is “really unconscionable,” said Dr. Peter Chin-Hong, an infectious disease specialist at the University of California, San Francisco.

Making it more difficult to schedule a shot may discourage even more people from getting vaccinated, doctors said.

“It’s just raising more and more barriers,” Dr. Chin-Hong said. “It’s like an obstacle course.” He added: “I don’t know anybody who’s not confused.”