The acting head of the Centers for Disease Control and Prevention has canceled the publication of a study that found that the Covid vaccine sharply cut the odds of hospitalizations and emergency visits last winter, a Health Department spokesman said.

Dr. Jay Bhattacharya, who has been overseeing the agency’s operations in the absence of a director, objected to the study’s design, saying it painted an inaccurate picture of the vaccine’s effectiveness.

The study, conducted by C.D.C. scientists, calculated the effectiveness of Covid shots by looking at the vaccination status of people who had sought care at hospitals and emergency rooms. It found that vaccination cut the likelihood of emergency visits due to Covid by 50 percent and of hospitalizations by 55 percent, according to a summary of the study viewed by The New York Times.

It was scheduled to be published on March 19 in The Morbidity and Mortality Weekly Report, the C.D.C.’s flagship journal. News of its cancellation was reported earlier by The Washington Post.

Some former C.D.C. officials said it was unusual for the head of the agency to cancel a scientific publication that had already been cleared by the agency’s staff scientists and had been scheduled for publication.

“I’ve never seen a case where an article in the M.M.W.R. that got to that stage was not published,” said Dr. Michael Iademarco, who led the center that included the publication’s operations from 2014 to 2022.

Andrew Nixon, a spokesman for the Department of Health and Human Services, said that “scientific reports are routinely reviewed at multiple levels to ensure they meet the highest standards before publication.”

He said that assessment “identified concerns regarding the methodological approach to estimating vaccine effectiveness, and the manuscript was not accepted for publication.”

The approach employed in this research has been used for years by scientists at the C.D.C. and elsewhere to gauge the real-world performance of flu and Covid vaccines, said Dr. Fiona Havers, a vaccine expert who resigned from the agency in June.

“It is really surprising that Jay Bhattacharya is now having issues with this methodology, since it has been a well-accepted standard for a long time,” she said.

A Health Department official, speaking on condition of anonymity to discuss internal agency matters, said Dr. Bhattacharya had met with the study’s authors but that they had not wanted to change its design.

Dr. Havers said it was impractical, if not impossible, to change the approach.

“The platform is designed in a certain way to collect data,” she said. “The data collection has happened, and they had done a full analysis using the methods that this platform has been using for years.”

The same method was also used in a study of the flu vaccine published last month. Had Dr. Bhattacharya been at the agency’s helm at that time, he would have raised objections to that report as well, the Health Department official said.