The federal watchdog, which is set to release the report in March, has spent the past several weeks meeting with statisticians at the CDC and in HHS to question officials about how they collect data. Three senior administration officials with direct knowledge of those conversations said that GAO raised concerns about the fact that health agencies are still not coordinating on tracking Covid-19 health indicators and that the data is incomplete and often inaccurate, especially when compared to state health data.

While there is significant overlap between the CDC and its parent HHS on Covid-19 data collection, the CDC has taken charge in tracking Covid-19 deaths and cases as well as vaccinations while HHS has focused on testing, hospitalizations and supplies.

GAO has previously criticized the federal government’s Covid-19 data collection and analysis. In January, the watchdog said in a report that “the federal government generally lacks consistent and complete COVID-19 data.” That report focused on HHS and its testing, case and hospital data collection. The March report is set to focus heavily on the CDC’s data, particularly the way it tracks Covid-19 deaths, cases and vaccinations, and will scrutinize why the agency is still struggling to improve its data.

The federal watchdog has previously released several comprehensive reports examining the implementation of the CARES Act, the $2.2 trillion relief package signed into law in March 2020 to manage the economic fallout of the pandemic. GAO made several recommendations throughout the last year in an attempt to guide federal agencies’ responses to the pandemic.

In a September report, GAO said the CDC needed to “involve key stakeholders to completely and consistently collect demographic data, and take steps to ensure its ability to comprehensively assess the long-term health outcomes of COVID-19 patients, including by race and ethnicity.” Then, in January, GAO said HHS should immediately “systematically review and inform the alignment of ongoing data collection and reporting standards for key health indicators.”

GAO’s upcoming report will be broader in scope and will cover topics such as the Department of Veterans Affairs' response to the pandemic, vaccines, nursing homes and infection control, testing and Medicaid spending. But it will also include a section that focuses on health indicators and CDC’s data efforts, pulling from interviews with people from within the agency and other health experts. One of the ideas proposed by those experts included creating a national dashboard that includes multiple health indicators to give Americans a clearer picture of the current state of the pandemic.

CDC officials are wary of making any sudden changes to the way they deal with data, primarily because the pandemic is still ongoing and updating systems and procedures in real time could create confusion.

The agency is already dealing with data accuracy issues, most recently around syncing state vaccination numbers with the agency’s own database. After continuous complaints from governors about the the CDC vaccine tracker, the agency is working to improve the way it displays vaccine doses allocated, shipped and administered, and coordinate more closely with state health agencies.

The agency has also created a new application that allows jurisdictions to submit data on the priority groups for the federal program to distribute vaccines through pharmacies. CDC has created a way to identify where “unaccounted doses” exist within a given jurisdiction, according to an internal memo obtained by POLITICO. The memo said the agency is also trying to improve its understanding of who has been vaccinated within each jurisdiction as a way to improve its reporting of Covid-19 race and ethnicity data.

CDC officials said they are fearful of any new recommendations that would alter their normal operations, particularly after what happened when the Trump administration introduced the HHS Protect data platform. That system pulls data about Covid-19 cases from federal and state agencies and from hospitals. It allows various officials, doctors and scientists access the system to make decisions on anything from treatment options to reopening.

Instead of submitting their data through the CDC, the HHS Protect system forced hospitals to manually submit their data to Teletracking, a private contractor that received a bid from HHS to develop the HHS Protect system. CDC officials said they were cut out of the reporting process and therefore could not ensure the data was accurate.

The same scenario could play out again if the agency is asked to streamline their efforts by partnering with out groups or institutions, officials said.

“I know people think this could make things more efficient,” one senior health official said. “But it could actually just make the data less reliable.”