FDA along with other government agencies, began to orderly shutdown on Wednesday Oct. 1, following Congresses’ failure to pass appropriation bills or continuing temporary resolution to keep agencies funded. FDA mentioned on its website the agency will continue operations under the extent permitted by law, addressing activities necessary to address imminent threats to the safety of human life and activities funded by carryover user fee funds.¹ FDA’s website directly addressed its limitations during the “lapse period,” saying, “All our work is important, but only some of our work is permitted to continue during a lapse in funding.”¹

What are FDA’s capabilities during the lapse period?

According to FDA’s website, the agency will continue vital activities to the extent permitted by law, that are critical to ensuring public health and safety in the U.S including the following.

• Maintaining core agency functions handling and responding to emergencies, such as monitoring for and quickly responding to outbreaks related to foodborne illness and the flu
• Supporting high-risk food and medical product recalls
• Pursuing civil and criminal investigations when FDA deems public health is imminently at risk
• Screening imported food and medical products
• Addressing other critical public health issues that involve imminent threats to the safety of human life
• Surveillance for significant safety concerns with medical devices and other medical products

FDA not accepting new drug applications

Additionally, the Human and Health Services (HHS) website touched on FDA’s abilities during the lapse period,mentioning that FDA is unable to accept new drug applications, generic drug applications, biological product applications, biosimilar biological product applications, animal drug applications, or medical device submissions that require payment of a user fee.² This is expected to delay the availability of these critical medical products, along with FDA's Human Drugs Program immediately halting most unapproved prescription drugs activities. ² The reason behind the stoppage in acceptations is due to FDA’s lack of legal authority to collect user fess during the lapse period, according to FDA’s website.¹

“However, during the lapse period, the FDA will not have legal authority to accept user fees assessed for FY 2026 until an FY 2026 appropriation or Continuing Resolution for the FDA is enacted. This will mean that the FDA will not be able to accept any regulatory submissions for FY 2026 that require a fee payment and that are submitted during the lapse period.”

User fee funds specifically support the review and marketing authorization of new medical products, the review of requests to conduct important clinical research, the issuance of certain guidance documents and regulations, along with other necessary activities aiming to help patients receive access to new therapies, diagnostics, vaccines, generics, biosimilars, and other medical products.²

With new submissions being halted, the agency’s plans released back in June of this year may be at risk. Back in June, FDA introduced the Commissioner’s National Priority Voucher (CNPV) program, designed to dramatically reduce the time it takes to review certain drug applications that align with critical US health and security objectives.³

FDA’s contingency staffing plan

According to the HHS website, 13,872 (86%) of FDA staff will be retained, including 10,740 (66%) who are exempt due to their activities or position already being funded or otherwise exempted, and 3,132 (19%) who are excepted due to their activities or positions being deemed necessary by implication, or for the safety of human life or protection of property.²

Sources

1. FDA FY 2026 Lapse in Funding Information U.S Food and Drug Administration October 1, 2025 https://www.fda.gov/about-fda/fda-fy-2026-lapse-funding-information
2. Food and Drug Administration Human and health Services September 25, 2025 https://www.hhs.gov/about/budget/fy-2026-fda-contingency-staffing-plan/index.html