Unlike other agencies within the Department of Health and Human Services, the Centers for Disease Control and Prevention will be subject to significant “reductions in force” if the government shuts down because of a funding lapse midnight Tuesday.

Of the 8,742 CDC workers slated to be furloughed, 1,563 are subject to the layoffs, according to the department’s plans.

A segment of the CDC workforce is protected from layoffs under a modified preliminary injunction issued by a U.S. District Court judge in August. The CDC has not said whether that applies to the workers listed in reduction-of-force status, or if they would be laid off if the injunction is lifted. The case challenging federal government layoffs, is pending.

An HHS official said Monday that staff will receive further guidance on specific contingencies for the agency.

The potential layoffs come at a tumultuous time for the CDC, after director Susan Monarez was removed less than a month into the job and other top officials left, sparking a clash with HHS Secretary Robert F. Kennedy Jr. over vaccine guidance and the agency’s direction.

Kennedy said earlier this month that “over the decades, bureaucratic inertia, politicized science and mission creep have corroded that purpose and squandered public trust” at the agency. He blamed the agency’s COVID-19 guidance for sowing distrust.

In August, a gunman angry about COVID-19 vaccines fired hundreds of rounds into the CDC headquarters in Atlanta.

HHS has roughly 80,000 employees. According to shutdown contingency plans, about 41 percent would be furloughed if current appropriations lapse. That works out to 32,460 employees who would be placed on temporary non-duty, non-pay status if Congress does not pass legislation to extend government funding. The guidance does not mention the potential for reductions in force in other divisions.

The CDC and the Agency for Toxic Substances and Disease Registry would retain about 36 percent of employees, according to the plan.

The retained staff would continue their work to combat disease outbreaks and support the World Trade Center Health Program, Energy Employees Occupational Illness Compensation Program Act, Vaccines for Children program and the President’s Emergency Plan for AIDS Relief.