FDA, Imports, and USDA: What Today’s Federal Shutdown Means for You

Bottom line up front: FDA will keep working on carryover user-fee–funded activities and life-safety work, but it cannot accept new user-fee submissions during the shutdown. Import screening at the border continues, though expect delays. Many USDA APHIS Veterinary Services (VS) functions tied to user fees (including animal import/export services) continue; other routine activities pause. Meat/poultry/egg inspections (USDA FSIS) continue as essential. (HHS.gov)

What’s actually shut down?

At 12:01 a.m. ET today (Oct. 1, 2025), the federal government entered a shutdown after Congress failed to pass FY 2026 funding. Expect agency-by-agency slowdowns and selective furloughs until funding is restored. (The Washington Post)

FDA: What continues—and what stops

Continues (exempt/excepted):

• Work funded by carryover user fees (e.g., certain reviews and marketing authorizations for drugs, biologics, devices; tobacco regulation).
• Life-safety functions: outbreak response, recalls, drug shortage mitigation, adverse event surveillance, review of import entries to identify health risks, and for-cause and certain surveillance inspections.
• FDA reports retaining ~86% of staff as exempt/excepted during a lapse. (HHS.gov)

Paused/limited:

• FDA cannot accept new submissions that require payment of a user fee (e.g., NDAs/BLAs/ANDAs, biosimilars, animal drug applications, device submissions with fees).
• Many routine inspections and longer-term policy and regulatory science projects are paused unless tied to carryover fees or life-safety needs. (HHS.gov)

Practical effect for sponsors: if your filing requires a fee, don’t attempt to submit today; the agency cannot accept it during the lapse. Time-sensitive interactions not tied to fees may still face delay.

Imports: FDA review and CBP operations

• CBP is open: Cargo processing and tariff collections continue, as inspection and law-enforcement functions are considered essential. Expect normal acceptance of entries but potential slower back-office actions (e.g., some audits/rulings) across trade agencies. (Reuters)
• FDA at the border: The agency continues import entry screening and high-risk exams to protect public health; routine throughput may slow if staffing is constrained. Prior Notice systems remain integral to targeting and exams. (HHS.gov)

Importers should anticipate longer exam/release timelines, especially for higher-risk commodities, and plan for contingencies if goods are flagged.

USDA snapshot—APHIS VS permits and FSIS inspections

• USDA APHIS (including VS) will continue activities supported by user fees, including animal import and export services, after-hours AQI services, and phytosanitary certifications. APHIS also continues animal/plant health emergency programs using no-year funds (e.g., HPAI, ASF). Routine activities funded solely by annual appropriations (e.g., some program ops, certain veterinary biologics reviews) cease during the lapse. (USDA)
• USDA FSIS food safety inspections (meat, poultry, egg products) continue as essential operations to protect public health. (USDA)

For VS permits (e.g., VS 16-3/16-6 series via APHIS eFile): processing that is fee-funded should continue, though users may still see slower turnaround due to broader staffing constraints elsewhere in the Department. (USDA)

How to Prioritize Regulatory Issues During a Federal Shutdown

During a federal government lapse in appropriations, importers of regulated goods face significant operational uncertainties at U.S. border entry points. Although essential border security and entry screening continue, reduced administrative staffing often leads to severe delays for import shipments. When border inspections encounter backlog or documentation issues, importers may need to prepare a CBP petition for relief from import refusal. Perishable goods governed by federal safety standards are especially vulnerable, requiring close monitoring under food and beverage compliance protocols. Importers handling livestock or animal-derived ingredients must also track user-fee services for animal products. Proactive communication with customs brokers is crucial during federal funding lapses.

While user-fee-funded carryover activities permit specific agency operations to continue, processing for new user fees usually stops during a government shutdown. Securing strategic FDA regulatory guidance allows businesses to rank pending submissions effectively and navigate supply chain disruptions. Medical device sponsors preparing fee-bearing premarket notifications can use the pause to finalize documentation for the FDA 510(k) clearance process so submissions are ready when the agency resumes accepting them. 

Organizations should create contingency strategies for managing prolonged holds and port storage fees. Keeping precise documentation and verification records reduces the likelihood of entry holds caused by administrative disruptions.

Successfully managing import delays during a federal government shutdown demands a dynamic legal and regulatory approach. Our experienced legal team offers real-time guidance to assist importers in overcoming port delays and mitigating agency backlogs. We work alongside businesses to liaise directly with customs authorities, ensuring entry holds are resolved efficiently. If your shipments face disruptions due to government shutdown delays, please contact us for prompt legal assistance.

Sponsor & Importer Checklist (actionable steps)

1. Hold fee-bearing FDA submissions until funding resumes; coordinate target dates with your reviewers. (HHS.gov)
2. Triage regulatory timelines: re-sequence milestones (e.g., PAIs/routine audits) likely to be delayed; keep “for-cause” readiness intact. (HHS.gov)
3. For imports, build slack into lead times; pre-clear documentation; ensure Prior Notice data quality; coordinate closely with your broker on port conditions. (Reuters)
4. Animal/biologic movements: if you rely on USDA VS permits, file promptly via APHIS eFile and flag any time-sensitive shipments; confirm whether your request is user-fee–funded (more likely to proceed). (USDA)
5. Communicate internally: update commercial, supply-chain, and quality teams on likely delays and what can still move (e.g., FDA import screening continues; FSIS inspections continue). (HHS.gov)

A note on timing and backlogs

Even where work continues, expect slower response times and growing queues. Once funding is restored, agencies typically prioritize life-safety and statutory-deadline work first, with catch-up on routine reviews and policy projects thereafter. Monitoring port conditions and center-specific communications remains critical. (HHS.gov)

Key sources we’re watching

• FDA (HHS) FY 2026 Contingency Staffing Plan – FDA (what continues/pauses; 86% staff retained; import entry review continues; user-fee submission acceptance paused). (HHS.gov)
• DHS/CBP statements confirming continued cargo processing and tariff collections during the shutdown. (Reuters)
• USDA Lapse of Funding Plan (FY 2026) detailing APHIS user-fee–funded continuity (animal import/export services) and FSIS essential inspections. (USDA)

If you have a time-critical filing, shipment, or permit need, reach out—we’ll help sequence next steps based on your facts and the latest center/agency posture.