On September 29, 2025, HHS released its updated fiscal year (FY) 2026 shutdown contingency plan outlining operational impacts in the event of a government shutdown. HHS estimates that 47,257 employees will be retained while 32,460 will be furloughed, meaning approximately 59 percent of staff will remain on duty. Within the department, CMS and the Health Resources and Services Administration (HRSA) are each expected to retain 53 percent of their respective workforces. Recent guidance from the Office of Management and Budget (OMB) encourages agencies to consider reduction in force (RIF) notices for employees in programs that lack discretionary funding or are not aligned with current administration priorities. This marks a departure from previous shutdown protocols, which typically involved temporary furloughs with reinstatement upon the resumption of funding. The final staffing impact of the shutdown may vary depending on further actions by OMB.
According to the plan, CMS will continue essential functions such as administering Medicare and Medicaid, conducting fraud and abuse-related activities, operating the Center for Medicare & Medicaid Innovation (CMMI), and managing Federal Marketplace activities including eligibility verification. Federal funds are sufficient to cover Medicaid for the first quarter of FY 2026, and CMS will retain staff to ensure Children’s Health Insurance Program (CHIP) payments to states. However, certain activities will be paused, including oversight of Medicare Administrative Contractors, operation of the Medicare call center, policymaking, rulemaking, and beneficiary casework.
HRSA programs supported by carryover funding, mandatory appropriations, or user fees will continue, including the THCGME, Medical Student Education, and Family to Family Health Information Systems. Activities including the Vaccine Injury Program and administrative contracts will be delayed.
The HHS contingency staffing plan can be found here.