The 2025 U.S. government shutdown kicked in effective at 12:01am, October 1, 2025, and as of this posting, has been in place for over a week.  The shutdown will continue indefinitely until Congress unifies and resolves the budget impasse.

The U.S. Food and Drug Administration (“FDA”), tasked with protecting public health by ensuring the safety, effectiveness and quality of drugs, biologics, medical devices, food and other regulated products within the broader Department of Health and Human Services (“HHS”), will undoubtedly experience disruptions on its operations in this period. 

FDA is not expected to go dark completely.  The FY 2026 HHS Contingency Staffing Plan[1] and the FDA-specific contingency plan[2] released right before the shutdown lay out how the Department and FDA will operate in the absence of enacted annual appropriations.  These plans provide a roadmap to ensure most of FDA’s core functions continue to operate during this time.  This is achieved through two main mechanisms: (1) exempting activities funded through carryover user fee funding and other unlapsed funding; and (2) relying on exclusions in the Anti-Deficiency Act (“ADA”) to continue activities related to imminent threats to the safety of human life or protection of property. Under the umbrella of these exemptions and exclusions, a majority (86%) of FDA staff are expected to be retained during the lapse.  This, however, does not obscure the fact that a significant number of FDA’s responsibilities will be constrained by the lapse.  Such responsibilities are still critical to protecting and promoting public health. 

User-Fee Funded versus Non-Fee-Funded Activities

FDA operations are sustained by a mix of congressional appropriation and statutory industry user fees, such as PDUFA, GDUFA, BsUFA, MDUFA and TUF.  The contingency plans make clear that FDA activities supported by user fees will continue as long as carryover balances remain. This includes many key functions performed by CDER, BDER, and CDRH for the regulation of drugs, biologics, and medical devices, and all activities relating to the regulation of tobacco products by CTP.  Specifically, FDA will continue to review pending NDAs, ANDAs and BLAs for market approval (but not accepting new applications), review IND submissions to support clinical trials, issue certain guidance documents and regulations, and other necessary activities to help patients have access to new therapies, diagnostics, vaccines, generics, biosimilars, and other medical products.  Therefore, for the sponsors whose interested FDA activities fall under the cover of user fees, the current shutdown may mean only minor delays.  The true risk is with time: as the shutdown drags on it drains the carryover balances.

There are also FDA activities and programs that are critical to FDA’s services to protect and promote public health and safety but nonetheless are not user fee funded.  According to the contingency plans, these activities are to be delayed or paused during the shutdown, other than in face of imminent threats to safety of human life and property.  Among them, FDA’s entire Human Foods Program (“HFP”) lacks user-fee funding and presents a notable vulnerability. 

HFP serves to oversees the safety, nutrition, labeling, and standards for the U.S. human food supply.  It is closely tied to HHS policy initiatives, including efforts to change the GRAS standard and eliminate potentially harmful ingredients (food dyes) from the supply chain.   However, according to FDA’s own plan, “food safety efforts within FDA’s Human Foods Program (HFP) would be reduced to safety surveillance and emergency responses. Longer-term food safety initiatives, including policy work to help prevent foodborne illnesses and diet-related diseases, would be halted, jeopardizing public health.”  The plan essentially cuts back HFP down to the most urgent tasks qualified for ADA exclusions, such as recalls, outbreak responses to foodborne illness and infectious diseases, and “for-cause” inspections.  This highlights FDA’s concern expressed in the plan that “in the event of a lapse in appropriations, FDA’s ability to protect and promote public health and safety would be significantly impacted, with many activities delayed or paused.”

Inspections and Enforcement

FDA conducts several types of inspections in connection with its regulation of food and medical products, including routine surveillance inspections, for-cause inspections, application-based inspections, and follow-up inspections.  The HHS plan makes it clear that “for-cause” inspections will continue during shutdown, while most routine surveillance inspections may not.  Similarly, the FDA plan limits “the number and type of inspections to be conducted, unless the inspections are for cause or otherwise necessary to detect and address imminent threats to the safety of human life, or can be conducted with carryover user fee funding.” Therefore, it raises operational and compliance questions about what inspections FDA will deem mission critical and whether it will have the resources necessary to facilitate those inspections. Specifically:

  • Will it conduct prior-approval inspections necessary to approved new drug applications?
  • Will it conduct inspections of foreign and/or domestic food, device, and drug manufacturers that are required to be inspected regularly to ensure a safe and robust supply chain?
  • What if there are insufficient resources to conduct both?

These open questions inject significant uncertainty during the shutdown, and companies should be prepared for unpredictable inspection scheduling and shifting enforcement priorities in this period.

Conclusion

FDA will not close its door entirely during the government shutdown, but its ability to function uniformly across the centers and programs to carry out all its regular activities is greatly hindered.  Ten days into the shutdown, there are still many open questions as to how FDA’s operations set out in the contingency plans unwind in the real world. Players in regulated industries should anticipate delays, closely monitor its communications with FDA, and be prepared for scheduling and priority changes for inspections.

Should you have any questions about how the shutdown may impact your business, please contact the authors of this article.

[1] https://www.hhs.gov/about/budget/fy-2026-hhs-contingency-staffing-plan/index.html

[2] https://www.hhs.gov/about/budget/fy-2026-fda-contingency-staffing-plan/index.html