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“Centralizing control of all data under the umbrella of an inherently political apparatus is dangerous and breeds distrust,” said Dr. 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 its basic job.”

The shift grew out of a tense conference call several weeks ago between hospital executives and Dr. Deborah L. Birx, the White House coronavirus response coordinator. After Dr. Birx said hospitals were not adequately reporting their data, she convened a working group of government and hospital officials who devised the new plan, according to Dr. Janis Orlowski, the chief health care officer of the Association of American Medical Colleges, who participated in the group’s meetings.

While she said she understood Dr. Lurie’s concern, Dr. Orlowski said the administration had pledged in “a verbal discussion” to make the data public — or at least give hospitals access to it.

“We are comfortable with that as long as they continue to work with us, as long as they continue to make the information public, and as long as we’re able to continue to advise them and look at the data,” she said, calling the switch “a sincere effort to streamline and improve data collection.’’

The change exposes the vast gaps in the government’s ability to collect and manage health data — an antiquated system at best, experts say. The C.D.C. has been collecting coronavirus data through its National Healthcare Safety Network, which was expanded at the outset of the pandemic to track hospital capacity and patient information specific to Covid-19.

In its new guidance, Health and Human Services said that going forward, hospitals should report detailed information on a daily basis directly to the new centralized system, which is managed by TeleTracking, a health data firm with headquarters in Pittsburgh. However, if hospitals were already reporting such information to their states, they could continue to do so if they received a written release saying the state would handle reporting.

Senator Patty Murray of Washington, the top Democrat on the Senate health committee, has raised questions about the TeleTracking contract, calling it a “noncompetitive, multimillion-dollar contract” for a “duplicative health data system.”