State health leaders, public health experts and hospital officials warn that an abrupt change in how the Trump administration requires them to report coronavirus data will increase the burden on facilities already strained by the pandemic and could impede the distribution of critical medicines.

The opposition came after the Department of Health and Human Services notified governors and hospital leaders this week that it was changing the protocol for sending the federal government daily information about coronavirus patients, supplies and bed capacity. Administration officials say that replacing a data-collection system run by the Centers for Disease Control and Prevention would streamline reporting and lead to more efficient distribution of therapeutics, testing supplies and protective gear.

Officials also suggested that states might want to get the National Guard to assist hospitals — an idea the industry has condemned.

The new rules took effect Wednesday and will determine the allocation starting next week of critical supplies from the federal government, including protective gear and remdesivir, an antiviral medication that is one of the only approved treatments for covid-19 patients. Senior HHS officials contended Wednesday that the switch was made with the agreement of the CDC, which no longer is a recipient of the information.

Critics, however, say they fear the elimination of the CDC’s role as a main data-keeper for the pandemic will be damaging, depriving states, hospitals and others of frequent analyses of data about the virus’s path in their communities. Smaller hospitals, in particular, are ill-equipped to suddenly adopt new data methods, critics said, though the industry has pledged to comply with the change.

“Especially when we are trying to be saving lives … it can be quite an undertaking,” said Carrie Kroll, vice president of advocacy, quality and public health for the Texas Hospital Association, many of whose members are overwhelmed as the virus surges in that state.

She said the order Wednesday to shift to the new data-reporting method happened with little notice or time for retraining. “On Monday we were alerted it was happening, On Tuesday, hospitals got an email as to what would change.”

Until Wednesday, Texas hospitals sent to the state all coronavirus data requested by state health officials and the federal government, and the state forwarded it to Washington. Suddenly, with the federal requirements expanded, hospitals must return to sending data separately to both places.

Bruce Meyer, president of Jefferson Health in Philadelphia, said the CDC’s data collection and analyses have been “highly reliable and efficient. Sidestepping these established tracking systems creates deep concerns that we will be unable to obtain appropriate and relable information to perform research and manage our response to the virus.”

During a telephone call between federal and state leaders Tuesday, several state health officials raised concerns about the additional burden placed on hospitals and the potential that late reporting would jeopardize allocation of critical medicine.

“The fact the federal government chose to change the reporting requirements right in the middle of the day, before the allocations are done, and therefore we don’t get allocation that we need based on the burden of disease that we have, that’s going to be really problematic for everybody,” said one state official from Texas. The Washington Post obtained a recording of the call but was unable to identify the official.

A Tennessee representative, who did not identify herself, told HHS officials that the short turnaround time could affect patient care. Not all hospitals have the same personnel do data reporting, she said. In places where resources are stretched thin, “they have to pull somebody from somewhere, which could very easily impede patient care and patient flow,” she said. “So I’m also kind of floored by the short turnaround time and some of the stuff we have to report.”

Coast Guard Vice Adm. Daniel B. Abel, part of the HHS team overseeing the federal response to the pandemic, assured callers that federal officials know “your folks are overwhelmed with patients and you’re doing the best you can.”

In a briefing for journalists Wednesday, HHS and CDC officials said the change was necessary because hospitals will have to report additional data in the weeks and months ahead. When new treatments for covid-19, the disease caused by the coronavirus, are available, federal officials will need to know which areas have greatest demand so they can be distributed in a timely way, said CDC Director Robert Redfield.

Under the new system, hospitals can report directly to the federal contractor, called Teletracking, or to their state health departments.

Under the reporting system that ended Wednesday, about 3,000 hospitals — or the health systems that own them — sent detailed information about covid-19 patients and other metrics to the CDC’s long-standing hospital network, the National Healthcare Safety Network, or NHSN. CDC staff analyze the data and provide tailored reports to every state twice a week and multiple federal agencies every day, according to a federal health official who spoke on the condition of anonymity to discuss policy deliberations.

Some health experts said they are worried the change will cut off their access to important data about covid-19 that has been housed until now by the CDC.

“We’re all very frustrated and very concerned. We use the [CDC system],” said Saskia Popescu, an infectious-disease epidemiologist at the University of Arizona. “We can pull data from [it] and extract reports. I have yet to hear if that’s possible for” the federal contracting system.

Georges C. Benjamin, executive director of the American Public Health Association, predicted that the data-reporting switch, “is not going to happen as easily or as well as they think.”

“I’m fundamentally against making changes in the middle of a disaster,” he said. “Changing data reporting, asking people to do a new task doesn’t go down easily.”

Benjamin represents one of six public health organizations that issued a statement Tuesday condemning the change.

In a letter to the nation’s governors this week, HHS Secretary Alex Azar and Deborah Birx, the White House coronavirus task force’s response coordinator, said the data that hospitals report Wednesday, Thursday and Friday this week will form the basis of federal distribution next week of remdesivir and other therapeutics and supplies. Hospitals were told that for the first days, they could focus on just seven of about 30 required data elements, including how much remdesivir they were using, along with admissions, adult patients and adults in intensive care with confirmed or suspected covid-19 cases.

Benjamin said he was doubtful the daily reporting would lead to more precise and efficient allocation of resources. The distribution “will fail,” he predicted. “Most of the people you are asking to give you the data will not have a clue what to do. The process has to get to the people who push the buttons, who write things in. That takes weeks of training.”

In the meantime, he said, “it means bad data in, bad distribution on the other end.”

Tom Nickels, the American Hospital Association’s vice president for government relations, said that although his members would comply with the change, hospitals are frustrated with repeated federal rule changes since the pandemic began. “It’s unfortunate they keep changing their mind,” Nickels said.

John Brady, vice president and chief financial officer for the Connecticut Hospital Association, said the latest change in requirements, on top of earlier ones, “is burdensome on hospitals, certainly those who are experiencing a crush of very ill patients from covid.”

Frances Stead Sellers and Isaac Stanley-Becker contributed to this report.