NIH Implements Contingency Plan as Government Shutdown Impacts Research Funding

In light of the recent US government shutdown, the National Institutes of Health (NIH) is rolling out a contingency staffing plan that will again affect funding. According to a statement released by the federal agency, 4,477 or 24.5% of its staff will be retained during the shutdown to maintain operations at the NIH Clinical Center.¹

In another staffing plan released by the US Department of Health and Human Services (HHS), it was revealed that 32,460 employees across the entire department will be furloughed during the shutdown.²

Continuing operations during the shutdown

“The NIH activities will continue to be largely centered on the ongoing operations at its biomedical research hospital, the NIH Clinical Center, to maintain the safety and continued care of its patients,” the recent NIH statement reads. “These patients are part of research focused on fostering fundamental creative discoveries, innovative research strategies, and improving human health. NIH will provide basic care services to protect the health of NIH animals and retain staff to safeguard ongoing experiments or operations, and facilities and infrastructure.”

Programs and activities put on hold

Activities that will not continue during this time at the NIH include:

• Peer review panels, advisory councils, new grant awards, and program management
• Admission of new NIH Clinical Center patients (except urgent cases)
• Launch of new clinical protocols and most intramural basic or translational research
• Graduate and postdoctoral training programs
• Scientific meetings and staff travel
• Veterinary and equipment services
• Most administrative, onboarding, mail, cafeteria, and visitor operations

Funding cuts and proposed restructuring under the Trump administration

This is the latest hit of many that medical research funding has absorbed since President Donald J. Trump’s inauguration in January. Just weeks later, the NIH announced that it would cut “indirect expenses” in the funding it provides to research grants by nearly half. Under the proposed policy from the time, the agency would cap these costs for all institutions at 15%. Immediately following, 22 states sued the NIH along with the HHS, citing the cut as unlawful.³

In a video interview with Applied Clinical Trials from earlier this year, Michael Liu, then medical student and researcher at Harvard Medical School, said: “It's not unreasonable to think that these cuts will have really impacted people in the clinical research industry, especially those who conduct trials. We know that trials are very expensive, and a loss of funding really compromises the ability to sustain and continue trials.”

Proposed NIH consolidation and congressional response

One of the Trump administration’s largest proposed slashes to NIH funding came earlier in May with the 2026 federal budget aiming to cut $17.97 billion from the agency. The proposal also aimed to consolidate the NIH from 27 centers and institutes at the start of 2025, down to just five:

• National Institute on Body Systems Research
• National Institute on Neuroscience and Brain Research
• National Institute of General Medical Sciences
• National Institute of Disability Related Research
• National Institute on Behavioral Health

A notable exclusion is the National Institute on Minority and Health Disparities, which would see $534 million in funding terminated due to its DEI nature.⁴

As of right now, the proposal is in flux as Congress rejected it in August and instead proposed a $400 million budget increase.⁵

Ongoing funding challenges for biomedical research

Despite these challenges for the NIH, a September 29 report from Nature revealed the agency was actually on pace to spend all of its $48 million budget by the end of the fiscal year on September 30. While the budget will be spent, it is funding far fewer projects as the White House directed the NIH to award large sums up front. As a result, success rates for grant applications sit at an all-time low.⁶

In his video interview with ACT, Liu concluded: “I think these cuts further potentially compromise the relationships and trust that we have with patients to continue to sustain the clinical trial enterprise.”

References

1. 2026. NIH Contingency Staffing Plan. HHS. Accessed October 7, 2025. https://www.hhs.gov/about/budget/fy-2026-nih-contingency-staffing-plan/index.html

2. FY 2026 HHS Contingency Staffing Plan for Operations in the Absence of Enacted Annual Appropriations. HHS. Accessed October 7, 2025. https://www.hhs.gov/about/budget/fy-2026-hhs-contingency-staffing-plan/index.html

3. Clinical Research, DEI Initiatives Caught in Political Headwinds Amidst Funding Freeze. Applied Clinical Trials. February 13, 2025. Accessed October 7, 2025. https://www.appliedclinicaltrialsonline.com/view/clinical-research-dei-initiatives-political-headwinds-funding-freeze

4. Masson, G. Trump plans $18B NIH budget cut, wants 27 centers consolidated into 5. Fierce Biotech. May 2, 2025. Accessed October 7, 2025. https://www.fiercebiotech.com/biotech/trump-plans-18b-nih-budget-cut-wants-27-centers-consolidated-5

5. Masson, G. Senate committee opposes Trump’s NIH cuts, proposes $400M budget increase. Fierce Biotech. August 4, 2025. Accessed October 7, 2025. https://www.fiercebiotech.com/biotech/senate-committee-oppose-trumps-nih-cuts-propose-400m-budget-increase

6. Kozlov, M. NIH races to spend its 2025 grant money — but fewer projects win funding. Nature. September 29, 2025. Accessed October 7, 2025. https://www.nature.com/articles/d41586-025-03168-4