Shutdown: FDA will not accept submissions requiring fees until funding resumes

Editor's note: this article's headline was updated on 2 October 2025 to clarify what submissions the agency would not be able to accept during the US government shutdown.

The US Food and Drug Administration (FDA) will only conduct vital and mission critical activities amid a government shutdown that began Wednesday after Congress failed to reach a deal to fund the federal government. During the funding lapse, FDA said it will not accept any regulatory submissions that require a fee.
 
The agency said that mission critical activities include responding to public health emergencies, supporting high-risk food and medical product recalls, and conducting essential surveillance of medical devices and other medical products.
 
The shutdown began Wednesday after the Senate failed to reach an agreement on a temporary spending package that would have funded the government until the end of November. The impasse was in part due to Senate Democrats’ refusal to accept a funding bill without an extension to Affordable Care Act (ACA) subsidies and a reversal of earlier cuts to Medicaid.
 
FDA said that during the funding lapse, it will not have the legal authority to accept user fees for Fiscal Year 2026 until an appropriations bill or Continuing Resolution is enacted. Consequently, the agency will be unable to accept any regulatory submissions that require a fee payment for FY 2026 if those submissions are made during the lapse period.
 
Shortly after the shutdown, FDA posted a message at the top of its homepage blaming the shutdown on Democrats. “Mission-critical activities of FDA will continue during the Democrat-led government shutdown. Please use this site as a resource as the Trump Administration works to reopen the government for the American people,” the message stated. Additionally, an email sent to all Health and Human Services (HHS) staff on Monday reviewed by Focus blamed Democrats for blocking the Continuing Resolution over “unrelated policy demands.”
 
According to FDA’s contingency plan for staff in the event of a shutdown, 13,872 employees, or 86% of employees will be retained, while 14% will be furloughed. Of the retained employees, 10,740 or 66%, are already funded or otherwise exempt from furlough, and 3,132 or 19%, are excepted as their activities are deemed necessary for the safety of human life. The contingency plan was released on 25 September.
 
The Department of Health and Human Services (HHS) will be more significantly impacted during this shutdown. According to the HHS contingency plan, of the 79,717 employees, 32,460 will be furloughed.
 
FDA announced that during the shutdown, “the agency will be continuing vital activities, to the extent permitted by the law, that are critical to ensuring public health and safety in the United States.”
 
These mission-critical public health activities include maintaining core functions to handle and respond to emergencies, such as monitoring and quickly responding to outbreaks related to foodborne illness and the flu, supporting high-risk food and medical product recalls, and pursuing civil and criminal investigations.
 
Other essential activities include screening food and medical products that are imported to the US, as well as conducting postmarket surveillance for medical devices and other medical products that pose “significant safety concerns.”
 
Steven Grossman, an FDA regulatory consultant and author of the FDA Matters blog, described the implications of the shutdown in a recent blog post.
 
He wrote that "with most of its employees retained, the FDA will be less affected than almost any other federal agency that doesn’t provide clinical services (VA, NIH Clinical Center, Indian Health Service).”
 
According to Grossman's blog post, those who have been furloughed are primarily concentrated in specific non-user fee functions. These include routine food inspections, developing guidance, database analysis, website management, and the roles of individuals responsible for accepting or disbursing funds, as well as various other administrative tasks.
 
FDA announcement on shutdown; FDA matters blog