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.

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 remdesivir, the first drug shown to be effective against the virus. But the Health and Human Services database that will receive new information is not open to the public, which could affect the work of scores of researchers, modelers and health officials who rely on C.D.C. data to make projections and crucial decisions…

News of the change came as a shock at the C.D.C., according to two officials who spoke on the condition of anonymity because they were not authorized to discuss the matter. 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.