The emergence of highly contagious Omicron subvariants this spring in the United States appeared to reduce the protection offered by vaccines against Covid hospitalizations, scientists from the Centers for Disease Control and Prevention reported on Friday.

But first and second booster shots helped to shore up people’s defenses, the agency found. The additional shots raised people’s levels of protection against those Omicron subvariants and restored some of the protection that was lost as time passed since their last shots.

“Booster doses should be obtained immediately when persons become eligible,” the C.D.C. scientists wrote.

The findings, however, came with a notable caveat: Measurements of vaccine effectiveness have been complicated by the number of unvaccinated people who have been infected by the virus, especially during the wintertime surge of Omicron cases.

Those prior infections give people some protection against Covid. As a result, in studies like the C.D.C.’s that compare outcomes from the virus in vaccinated and unvaccinated people, the vaccines appear less protective than they really are.

The C.D.C. scientists used what little information they had about patients’ infection histories to try to account for those difficulties. Using data from hospitals across 10 states, the agency’s scientists studied some 58,000 hospitalizations with a diagnosis of Covid-like illness from mid-December through mid-June. The study focused on adults with healthy immune systems.

By late April, subvariants of Omicron known as BA.2 and BA.2.12.1 had outcompeted the version of Omicron that spread across the country over the winter.

After those subvariants became dominant, the Pfizer-BioNTech and Moderna vaccines were less effective in keeping people from being admitted to the hospital with Covid than they had been during the wintertime Omicron wave, the study found.

Two doses of the vaccines were 24 percent effective against hospitalizations after the variants took over, compared with 61 percent during the period when the original version of Omicron dominated. (Those figures held for people who had been given their second dose at least five months earlier.)

That decline probably partly resulted from the ability of the subvariants to evade people’s immune defenses from the vaccine, and partly from unvaccinated people drawing some protection from earlier infections.

A booster dose helped considerably, even though the benefits of those additional doses appeared to wane over time. Once the subvariants became the main sources of infection, a third dose of Pfizer or Moderna raised the vaccines’ effectiveness against hospitalization to 69 percent initially, and 52 percent after four months or more.

The third doses had been even more protective during the wintertime surge of the original version of Omicron.

Second boosters were authorized in late March for people 50 and older with healthy immune systems, and those additional boosters appeared to help people weather the subvariant surge, the C.D.C. found.

At least a week after a fourth dose, the vaccines were 80 percent effective against hospitalizations with Covid, the agency said. That was a considerable lift from the 55 percent effectiveness offered by three doses after four months in that age group.

It was not clear how quickly the protection offered by that fourth dose would diminish. The study also did not measure the vaccines’ performance against BA.5, the latest Omicron subvariant, which appears to be driving a fresh surge of cases and hospitalizations. That subvariant has become dominant among new U.S. cases and appears to be the most evasive form of Omicron to spread in the country.

With hospital admissions rising, federal health officials have urged eligible people to get booster doses as soon as possible, saying that those shots would not prevent people from getting an additional dose of an updated, variant-specific vaccine in the fall or winter. The latest results reinforced the need for booster shots, the agency said.

“Given recent increases in deaths and hospitalizations associated with the BA.5 variant,” the C.D.C. said on Friday, “everyone should stay up to date with recommended Covid-19 vaccinations, including additional booster doses for those who are moderately to severely immunocompromised and adults over 50.”