The Food and Drug Administration announced it will not accept new drug applications during the federal government shutdown that began Wednesday, marking the first such closure in nearly seven years and potentially delaying critical pharmaceutical submissions from major industry players.
In a statement referenced by Leerink Partners, the FDA explained it cannot accept new drug applications because doing so would require accepting industry user fees assessed for 2026, which the agency is prohibited from collecting during this "lapse period." The analysts identified several companies that could be impacted by this restriction, including AbbVie, Amgen, Bristol Myers Squibb, J&J and Pfizer.
Operational Continuity Despite Shutdown
Despite the shutdown, the FDA will retain approximately 86% of its workforce, or 13,872 employees, according to agency guidance documents. This represents a significantly higher retention rate compared to previous shutdowns in 2012 and 2013, when a much smaller portion of the workforce remained operational.
"When FDA faced this situation in 2012 and 2013, a much lower portion of the workforce was retained," wrote Steven Grossman, policy and regulatory consultant, in his blog FDA Matters. He attributed the improved staffing levels to efforts by FDA Commissioner Marty Makary and his predecessors who "have pushed hard to have FDA positioned as a public health and public safety agency that is needed at all times, including during a shutdown."
About 66% of the retained staff are covered by user fees or other carryover funds, enabling continued operations for certain regulatory activities. The FDA can continue reviewing existing drug and medical device applications funded by user fees, as well as requests to conduct clinical research and work on certain guidance documents.
Limited Regulatory Activities
The agency will maintain only "activities necessary to address imminent threats to the safety of human life and activities funded by carryover user fee funds," according to its official statement. However, many regulatory functions will be suspended or reduced.
Food safety efforts will be curtailed during the shutdown, and the FDA will be unable to support much of its work protecting Americans from unsafe and ineffective compounded drugs. This suspension of compounding oversight is particularly significant given ongoing issues with compounded versions of popular GLP-1 obesity drugs.
Industry Impact and Duration Concerns
Leerink Partners consulted with former Senator Richard Burr and another senior counsel key opinion leader, who advised that the shutdown could last as long as a month if no resolution is reached within a week. The analysts noted that while existing FDA reviews will continue to be funded, "resultant noise may cause some delays."
The shutdown compounds existing challenges at the FDA, which has already experienced what one unnamed key opinion leader described as a "slowdown in FDA review processes, characterized by frequent breakdowns in communication between the FDA and applicants" since Trump took office.
TD Cowen analyst Rick Weissenstein noted that the current staffing numbers "reflect the impact of the significant job cuts at FDA early in the Trump Administration, with many non-user fee positions already eliminated." However, he suggested these earlier reductions might actually insulate the agency from further workforce cuts threatened by Trump.
Broader Healthcare Research Impact
Within the Health and Human Services umbrella, research dependent on National Institutes of Health grants for medical research will face the most significant disruption, according to the key opinion leaders consulted by Leerink Partners. The shutdown adds another layer of uncertainty to an already challenging year for FDA-regulated industries, which have faced layoffs throughout the Health and Human Services Department and the departure of many key FDA officials.
