More Than 40% of Federal Healthcare Workers Furloughed During Shutdown
Healio | By Gerard Gallagher, Caitlyn Stulpin, Sara Kellner & Fact checked by Kristen Dowd
October 1, 2025
The first government shutdown in almost 7 years began Wednesday after Congress was unable to come together on legislation to fund the federal government.
The disagreement between Republicans and Democrats centers on health care coverage, including Medicaid funding and whether to renew the enhanced premium tax credits that make coverage under the Affordable Care Act cheaper.
It is the 21st time the government has been shut down since 1977. The last shutdown was the longest in history, lasting 34 days from Dec. 21, 2018, to Jan. 25, 2019.
More than 32,000 HHS staff will be furloughed during the current shutdown — or about 41% of the nation’s federal health care workforce, the department said.
Below is a summary of staff and programs affected by the shutdown in several key health agencies, according to HHS.
CDC
Almost 65% of CDC staff will be furloughed during the shutdown, totaling more than 8,700 employees. Among the furloughed staff, more than 1,500 were part of the federal reduction-in-force (RIF) layoffs issued earlier this year.
Leading up to the shutdown, the White House threatened more federal RIFs if lawmakers are unable to strike a deal. A memo published online Wednesday said the Office of Management and Budget “has directed agencies to consider issuing RIF notices” to employees in programs, projects or activities “not consistent with the president’s priorities,” echoing language used to explain the mass layoffs within HHS in April.
During the shutdown, the CDC and the Agency for Toxic Substances and Disease Registry will stop providing guidance to state and local health departments for implementing public health programs, according to HHS. The CDC also will “not be able to provide communication to the American public about important health-related information” during the shutdown, and “critical” year-end surveillance reports will be delayed.
NIH
At the NIH, around 75% of staff will be furloughed during the shutdown, according to HHS. The rest “will continue to perform vital tasks related to imminent threats to human health or life, specifically by providing patient care,” the department said.
Although care for existing patients will continue, the shutdown will halt new admissions of patients at the NIH Clinical Center, and all training, travel and basic research services conducted by NIH scientists will be halted.
All grant peer review meetings, advisory council meetings and program and grants management activities also will be suspended.
FDA
Far fewer staff will be furloughed at the FDA, which can expect to retain around 86% of workers during the shutdown, according to HHS.
The workers who will remain in their jobs include “those whose work is necessary to address imminent threats to the safety of human life ... those whose work is necessary for the protection of property, and ... those whose work is ‘necessarily implied’ from the authorized continuation of other activities,” according to HHS.
During the shutdown, the FDA will stop accepting applications for new drugs, generic drugs, biological products, animal drugs or medical devices that require payment of a user fee. Additionally, the FDA will halt pre-market safety reviews of novel animal food ingredients for livestock, which means the agency will not be able to ensure the safety of meat, milk and eggs for human consumption.
CMS
A little over half (53%) of CMS workers will remain on the job during the shutdown, including all staff “who support activities that have funding available during a lapse in appropriations,” HHS said.
CMS expects delays in survey activities — such as recertification surveys and all surveys conducted by federal staff — as well as delays in rulemaking and policy development and the suspension of CMS beneficiary casework services and national and community outreach and education activities, according to HHS.
Other divisions
The Administration for Children and Families (ACF), which offers social and economic assistance to families, will continue its Unaccompanied Alien Children program, disaster recovery programs and the Federal Parent Locator Service, as well as grants that were awarded before the shutdown.
The Head Start program, which is part of ACF, is unlikely to be disrupted by the shutdown because its grants are awarded throughout the year, the deputy director of the National Head Start Association told U.S. News & World Report.
Most grants awarded through the Substance Abuse and Mental Health Services Administration began on Sept. 30 and will be able to continue during the shutdown, according to HHS. The services that will remain available include the Disaster Distress Helpline and the 988/Suicide Lifeline. People will also still be able to receive referrals for behavioral health concerns, and the administration will continue to respond to emergency requests through the Opioid Treatment Program.
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