Written by: Blaine Van Leuven, MS, MBA, RAC
Executive Director, Regulatory and Strategic Development
As of October 1, 2025, the U.S. government has entered a partial shutdown because Congress failed to pass the appropriation bills required for fiscal year 2026. Federal agencies have furloughed non-essential staff, while “essential” public health and safety functions continue.
When the U.S. government shuts down, the Food and Drug Administration (FDA) must scale back activities despite its public health mission. Drug developers should anticipate disruptions and plan accordingly. Most notably, the FDA Commissioner Martin Makery announced that the FDA will stop accepting new drug submissions for review while the government is shut down, but will continue to process existing drugs under review. This article highlights likely impacts on FDA operations and practical steps companies can take to minimize delays.
What Happens at the FDA During a Shutdown
The FDA does not stop working completely, but operations narrow. Roughly 85% of staff continue working, supported by carryover user fees. Critical work – such as addressing public health emergencies, adverse event monitoring, recalls, drug shortage mitigation, and “for-cause” inspections – continues.
Ongoing reviews of drug applications already under FDA review will proceed, funded by FY2024 user fees. However, communication from regulators may be slower than usual. Routine research, policy development, and most surveillance inspections are paused until appropriations resume.
User Fee Collections and Submissions
A major limitation is that FDA cannot collect new FY 2026 user fees until Congress passes an appropriation. For example, FDA recently confirmed that the Generic Drug User Fee Amendments (GDUFA) system is deactivated until funding is restored. By law, these fees are not due until either October 1 or the first business day after appropriations are enacted—whichever is later.
This means no GDUFA or PDUFA annual fees are payable until the shutdown ends. However, new submissions requiring user fees (NDAs, BLAs, ANDAs, biosimilars) cannot be accepted during this period. Applications filed electronically will sit in queue until the government reopens.
Non-fee submissions, such as Investigational New Drug Applications (INDs), may still be received. FDA indicates it will continue reviewing INDs, particularly those tied to urgent public health needs. Still, sponsors should prepare for delays in the initial 30-day review clock for standard INDs.
Key Impacts for Sponsors
- Ongoing reviews: Existing PDUFA and GDUFA application reviews typically continue, but responsiveness may be slower.
- New submissions: FDA cannot accept new applications-requiring fees until appropriations return.
- INDs and research: Non-fee submissions may move forward, but timelines could slip unless for urgent indications.
- Meetings: Scheduled FDA meetings may be affected; some may continue virtually or by teleconference, others postponed.
- Compliance and safety: Required reporting continues. FDA will still act on recalls, shortages, or imminent safety issues.
How Companies Can Prepare
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Adjust Timelines
If you plan to submit a major application such as an NDA or BLA, be prepared to delay or accept that the review clock won’t start until appropriations are enacted. Reassess your launch plans, milestones, and investor communications accordingly. For ongoing reviews, build flexibility into expectations, as communication may slow.
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Confirm Meetings
Check the status of scheduled FDA meetings. Teleconferences for PDUFA or other User-Fee programs may proceed, but in-person or lower-priority meetings could be rescheduled. Secure any needed guidance or minutes before staff availability becomes constrained.
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Maintain Compliance
Continue meeting all safety and reporting obligations. IND annual reports, safety reporting, pharmacovigilance submissions, and adverse event reporting remain mandatory. Quality standards (GMP, GCP) must be upheld. While routine inspections may be deferred, critical lapses will still draw immediate scrutiny. Treat this period as a test of your compliance systems.
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Monitor Fee Obligations
Annual user fee payments are delayed until appropriations resume. Do not attempt to pay fees while systems are disabled. Instead, prepare internally so payments can be processed quickly once due. Keep records of FDA’s correspondence and watch for notices on the reopening schedule. You can also reach out to the User Fee Helpdesk at (301) 796-7200 or [email protected].
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Plan for Recovery
Expect a backlog when operations restart. FDA systems will reactivate, and multiple sponsors will file applications that were placed on-hold during the shutdown. Prioritize your filings and be ready to act quickly. Document shutdown-related delays in case you need to explain program impacts to stakeholders.
Questions Sponsors Should Ask
- Do we have submissions planned during this period, and do they involve user fees?
- Are there FDA meetings or milestone dates coming up? Have we confirmed their status?
- Have we addressed all pending FDA information requests to avoid unresolved issues?
- Are compliance, pharmacovigilance, and safety monitoring systems fully operational?
- Are we prepared to pay user fees promptly once appropriations resume?
Conclusion
A government shutdown can create uncertainty, but it need not derail development programs. Critical FDA review work supported by existing user fees continues, while new submissions requiring fees must wait. By adjusting timelines, maintaining compliance, confirming engagements, and preparing for recovery, sponsors can limit the disruption.
Stay informed through FDA announcements and official guidance available on the FDA’s website. Ultimately, preparation and vigilance will allow drug developers to navigate shutdown conditions while safeguarding development progress and compliance.