Critics fear a new system for hospitals to report virus data could be open to political distortion.

The Trump administration has ordered hospitals to bypass the Centers for Disease Control and Prevention and, beginning on Wednesday, send all coronavirus patient information to a central database in Washington — a move that has alarmed public health experts who fear the data will be distorted for political gain.

The new instructions are contained in a little-noticed document posted this week on the Department of Health and Human Services’ website, Sheryl Gay Stolberg reports. From now on, H.H.S., and not the C.D.C., will collect daily reports about the patients that each hospital is treating, how many beds and ventilators are available, and other information vital to tracking the pandemic.

Officials say the change will streamline data gathering and assist the White House coronavirus task force in allocating scarce supplies like personal protective gear and the drug remdesivir. Some hospital officials welcome the move, saying it will relieve them of responding to requests from multiple federal agencies.

But public health experts have long expressed concerns that the administration is politicizing science and undermining the disease control centers; four former C.D.C. directors, spanning both Republican and Democratic administrations, said as much in an opinion piece published Tuesday in The Washington Post. The data collection shift reinforced those fears.

“Centralizing control of all data under the umbrella of an inherently political apparatus is dangerous and breeds distrust,” said Nicole Lurie, who served as assistant secretary for preparedness and response under former President Barack Obama. “It appears to cut off the ability of agencies like C.D.C. to do is basic job.”

The shift grew out of a tense conference call several weeks ago between hospital executives and Dr. Deborah Birx, the White House coronavirus response coordinator.

After Dr. Birx complained that hospitals were not adequately reporting their data, she convened a working group of government and hospital officials who devised the new plan, according to Janis Orlowski, chief health care officer of the Association of American Medical Colleges, who participated.

But news of the change came as a shock inside the C.D.C., which has long been responsible for gathering public health data, according to two officials who spoke on condition of anonymity because they were not authorized to discuss it. A spokesman for the disease control centers referred questions to the Department of Health and Human Services, which has not responded to a request for comment.

The dispute exposes the vast gaps in the government’s ability to collect and manage health data — an antiquated system at best, experts say.

Representative Donna E. Shalala, who served as health secretary under former President Bill Clinton, said the C.D.C. is the proper agency to gather health data and that if there are flaws in its systems, they should be fixed. “Only the C.D.C. has the expertise to collect data,” she said. “I think any move to take responsibility away from the people who have the expertise is politicizing.”