Hospitals have been ordered to bypass the Centers for Disease Control and Prevention and send all patient information to a central database in Washington, raising questions about transparency.

The new instructions were posted recently in a little-noticed document on the Department of Health and Human Services website. From now on, the department — not the C.D.C. — will collect daily reports about the patients that each hospital is treating, the number of available beds and ventilators, and other information vital to tracking the pandemic.

"Historically, C.D.C. has been the place where public health data has been sent, and this raises questions about not just access for researchers but access for reporters, access for the public to try to better understand what is happening with the outbreak," said Jen Kates, the director of global health and H.I.V. policy with the nonpartisan Kaiser Family Foundation.

"How will the data be protected?" she asked. "Will there be transparency, will there be access, and what is the role of the C.D.C. in understanding the data?"

Michael R. Caputo, a Health and Human Services spokesman, called the C.D.C.'s system inadequate and said the two systems would be linked. The C.D.C. would continue to make data public, he said.