FDA Contingency Plan (FY 2026)

The Food and Drug Administration (FDA) retained 86% of its staff, thanks in large part to user-fee funding which is collected from entities in industries under FDA jurisdiction. Though the FDA can use user fees previously collected to support continued operations, the FDA cannot collect any new user fees.

Staffing

Approximately 13,872 employees will continue to work. Of these, 66% are exempt (funded by user fees or other ongoing sources), while 19% are excepted staff handling critical functions.

Activities Continuing

• Reviews and approvals of medical products
• Oversight of tobacco products
• Issuance of certain guidance
• Reviews of requests for clinical research

The agency will also carry out emergency functions, such as recalls, outbreak response, import safety reviews, for-cause inspections, and criminal enforcement actions.

Activities Paused

• Acceptance of new drug, biologic, biosimilar, device, or animal drug applications that require user-fee payments
• Hiring, staff development, and laboratory investments in areas without carryover funding
• Oversight of unapproved and compounded drugs (unless tied to imminent threats to health or safety)
• Pre-market reviews of novel animal food ingredients and broader food safety initiatives (limited to emergency surveillance and responses)

CMS Contingency Plan (FY 2026)

The Centers for Medicare & Medicaid Services (CMS) core entitlement programs will proceed largely uninterrupted:

• Medicare: Operations will continue during the shutdown, though claims will be held for 15 days.

CMS shared:

“We’ve instructed the MACs to hold all claims with dates of service on or after 10/1/25. This is standard at the start of each quarter to allow for validation of quarterly system releases. The hold also helps prevent the need to reprocess large volumes of claims should Congress act after the statutory expiration date. We expect this to have minimal impact on providers, as the 14-day payment floor still applies. Claims for services not related to the extenders are anticipated to be released and paid immediately following the 14-day payment floor (which includes the 10-day hold). Decisions on claims tied to the extenders remain pending until the status of the legislation is determined.”

• Medicaid: CMS has sufficient funding to cover Medicaid for the first quarter of FY 2026 (Oct–Dec 2025) due to the advance appropriation included in the Full-Year Continuing Appropriations and Extensions Act, 2025. Payments to states for CHIP will also continue.
• Marketplace: Federal Marketplace activities, such as eligibility verification, will be supported by carryover user fees.

Staffing

CMS has retained 3,311 staff (53% of its workforce), including 3,105 exempt employees funded through nondiscretionary sources (such as user fees and mandatory programs) and 206 excepted staff who perform life-safety or property-protection functions. An additional 84 Commissioned Corps members will continue working.

Activities Impacted

• Facility surveys limited to the most serious complaints
• Delays in policy and rulemaking
• Scaled-back oversight of contractors (e.g., Medicare Administrative Contractors, call centers, and IT vendors)
• Suspension of outreach, education, and casework functions

NIH Contingency Plan (FY 2026)

Staffing

The National Institutes of Health (NIH) has retained 4,477 staff (24.54% of its workforce). Only five staff are exempt, with 4,472 designated excepted.

Activities Continuing

• NIH Clinical Center patient care
• Safety of animals and ongoing experiments
• Maintenance of infrastructure (labs, IT, property)
• Critical systems (clinical records, networks) needed for patient care and clinical trials

Activities Paused

• Peer review meetings, advisory councils
• Issuance of new grants or awards
• Admission of new patients (unless medically necessary) and initiation of new clinical protocols generally cease
• Basic and translational research, training programs, scientific meetings, travel, most administrative functions, and many veterinary services are curtailed or halted

Key Shutdown Resources & Links

• FY 2026 HHS Contingency Staffing Plan for Operations in the Absence of Enacted Annual Appropriations — Webpage outlining how HHS will operate in the case of a shutdown.
• FY 2026 HHS Contingency Staffing Plan for a Lapse in Appropriation — Summary chart of HHS contingency plans. In short, 59% of HHS employees will be retained and 41% will be furloughed.