Day 2 Shutdown Update: FDA, USDA, and Import Operations

As the federal government shutdown enters its second day, more clarity has emerged around the scope of disruptions across FDA, USDA, and import operations. While essential public health and safety functions continue, significant slowdowns and funding freezes are taking hold.

FDA

• No new user-fee submissions accepted: FDA has formally confirmed it cannot accept new drug, biologic, device, or other applications requiring fees during the lapse. Submissions already filed with fees paid may continue under carryover funding. Medical device companies preparing a new submission can use the pause to finalize predicate comparisons, testing documentation, and other materials with 510(k) premarket notification support, so the filing is ready once FDA resumes accepting fee-bearing submissions. 
• Workforce retained: Approximately 86% of FDA employees remain on duty as exempt/excepted, largely tied to user-fee programs and life-safety functions.
• Imports continue under strain: Import entry review and “high-risk” inspections remain active, but slower throughput and potential backlogs are expected at ports. Routine inspections and longer-term policy work are paused.

USDA

• Payments frozen: Commodity, conservation, disaster, and other farm program payments are suspended until appropriations resume. This is already impacting agribusinesses relying on cash-flow support.
• Furlough scale: Reports confirm ~42,000 USDA staff (about half of the workforce) are furloughed, significantly curtailing agency activity.
• Animal welfare oversight suspended: Routine Animal Welfare Act inspections have stopped, pausing oversight of breeders, exhibitors, and related facilities.
• Essential inspections continue: FSIS food safety inspections (meat, poultry, eggs) remain operational, and APHIS continues fee-funded import/export services.

Imports & Trade

• CBP operations continue: Cargo processing and tariff collections remain in place as essential functions.
• FDA screening continues: FDA continues entry review and targeted import exams, but staffing reductions mean slower release times are likely.
• Cross-agency delays possible: Coordination with USDA APHIS and other partner agencies could add further delays for shipments requiring multiple clearances.

How to Distinguish Shutdown Delays From Regulatory Issues

As the shutdown continues, importers should distinguish routine staffing delays from regulatory action. Companies moving imported goods should expect slower processing and coordinate with brokers. Animal-product businesses should also monitor animal product services. If an FDA refusal results in CBP liquidated damages, a CBP petition for relief may become relevant.

Reduced staffing does not suspend safety obligations for regulated businesses. FDA may continue activities involving product recalls, outbreak response, and other life-safety concerns. Food companies must therefore maintain food and beverage compliance even if routine agency oversight slows. Internal quality and response procedures should remain active throughout the funding lapse. A shutdown may delay medical device submissions without changing clearance requirements. An experienced FDA 510(k) consultant can help keep documentation ready for submission once FDA resumes normal intake.

Managing regulatory compliance during government disruptions requires experienced legal counsel to navigate shifting agency priorities. At FDA Atty, we help businesses assess whether a delay can wait or requires action now. That may include reviewing agency communications, import issues, or compliance obligations. If your company is facing uncertainty, contact our FDA regulatory attorneys for guidance; we are prepared to help you! 

Key Takeaways

• Expect delays at ports and in regulatory submissions requiring fees.
• Agricultural businesses should plan for suspended USDA payments and reduced program support.
• Animal and biologics operators relying on VS permits or inspections should confirm status via APHIS eFile and anticipate slower turnaround.
• Routine compliance oversight may be temporarily reduced, but high-risk enforcement and safety-related activities continue.

We will continue to monitor and provide updates as the situation evolves.