Part of the new project involves digitizing case reports for public health departments to assess the incidence of disease — already the focus of a nationwide public-private effort. HHS said the project is not duplicative.

The department still is trying to fix the hospital database, called HHS Protect, which hospitals and states were required to use with little warning last month. Hospital operators and state health departments have reported numerous technical burdens that have forced some hospitals to manually enter data about ICU beds and drug supplies, and have led to unexplained fluctuations in hospital occupancy posted on public dashboards.

The health department’s chief information officer, who oversaw that effort, abruptly resigned on Friday, after expressing surprise the project had drawn intense public scrutiny. Democrats have suggested the way the changeover bypassed a CDC reporting system was part of a pattern in which the White House has undercut the public health agency for political gain. HHS maintains the CDC has access to the HHS Protect database.

The White House coronavirus task force and HHS are assigning federal liaisons to state health departments in an effort to fill information gaps. HHS attributes problems to occasional errors, and says the system publishes “weekly estimates” that would reflect the state of play had all hospitals reported.

The administration is now pivoting from the turbulent aftermath of the reporting system to its broader ambitions for public health tech.

The new, broader data overhaul, called the Modernizing Public Health Reporting and Surveillance project, had a soft launch of sorts last week when federal officials began canvassing public health and tech communities, seeking participation in a pilot program.

HHS describes the project as a multi-year initiative to “improve data quality and information technology at state and local public health departments.”

A list provided to prospective partners for the pilot, obtained by POLITICO, describes a grab-bag of ideas, including automating hospital and lab reporting; moving to electronic case reporting; overhauling state and local data systems and digitizing mobile coronavirus test sites — among other ambitious tasks.

“We are now poised to move to automated data collection for the use of every relevant expert at HHS, particularly the CDC,” said HHS spokesperson Michael Caputo in a statement.

But skeptics say some of the work risks needlessly duplicating efforts already underway.

The new idea is “extremely ambitious,” said Michelle Meigs, a tech expert with the Association of Public Health Laboratories, who discussed the effort with the government.

“My biggest concern is undermining good work that is already happening: I made it clear on my call that this type of work has to be done in concert, not independent of initiatives that are already either mature and underway.” Meigs noted that there are infrastructure projects from electronic lab reporting to data transport and standards already ongoing in the field.

Some skeptics are also concerned about the role of the U.S. Digital Service, a technology unit within the White House that was established in the wake of the failed 2013 launch of the government’s Obamacare exchange, Healthcare.gov.

Observers say the team is technically savvy but lacks public health experience. “So egotistical to think they can ride in and solve problems that public health people have been trying to solve for years,” one HHS official said.

While the ideas described in the pilot project list target weaknesses in the system revealed by the pandemic, people with knowledge of the plan say they’re worried the team doesn’t have public health and clinical experience.

“USDS has a strong technical background but not in the public health area,” said one CDC official.

An HHS spokesperson contended that the USDS team has a wide variety of backgrounds, including in health IT and state and federal health agencies.

“We value our collaboration with federal partners on multiple health care projects over many years, and bring diverse experiences in health care and technology to these projects,” said a spokesperson for the USDS.

Meanwhile, problems from the HHS Protect rollout still haven’t been fully sorted out. Hospitals continue to complain the system is burdensome, and the project is still marred by inconsistencies and incomplete data.

“The hospitals are doing their best to comply with the federal and state reporting requirements, but it has certainly added an administrative and financial burden at the worst possible time for our hospitals,” Cara Welch, a spokesperson with the Colorado Hospital Association, wrote in an email.

HHS says that 85 percent of the nation’s hospitals report daily — a mark that is improving, and that includes more metrics the government uses to allocate scarce resources during the pandemic, like the drug remdesivir. But federal officials say they receive only half of the required clinical information on average, a gap that could distort the scope of the pandemic and obscure who’s getting sick where.

The Atlantic’s Covid Tracking Project, which monitors hospital data, compared reports since the changeover. It found last week “contradictions that suggest the federal data continue to be unreliable, while the state datasets face their own challenges.”

“Hospitalization data used to be really reliable with regards to understanding the burden on health care infrastructure in the United States. And it’s becoming less and less illuminating of a figure,” Jessica Malaty Rivera, the project’s science communication lead, told POLITICO.

The department has fiercely defended the change. “Using this new, innovative and flexible collection mechanism, we have far more Covid-related real data, far faster, giving us increased capacity for life-saving projects like therapeutics distribution,” Caputo said. The new system is more flexible, HHS officials say, allowing them to add fields tracking new types of data more readily.

Democrats in Congress are continuing to press the administration on its plans. Senate health committee ranking member Patty Murray (D-Wash.) and Senate Minority Leader Chuck Schumer last week released documents to the New York Times showing that TeleTracking, the private contractor whose technology underpins the portal through which hospitals report data, refused to answer questions about the project on the basis of a nondisclosure agreement.

The Times also obtained a letter that reflects deep discontent over the department’s tech work. Nearly three dozen current and former members of a federal advisory committee expressed alarm over bypassing CDC’s system, arguing it “will have serious consequences on data integrity.”