WASHINGTON — The National Institutes of Health has maintained a budget near $47.5 billion after Congress rejected the Trump administration’s proposed 41% cut for fiscal year 2026. But researchers and former NIH officials say the headline figure obscures a slower and more politically controlled grant process that is disrupting laboratories, clinical studies and training programs nationwide. More than 80% of NIH funding is distributed through grants. Those awards support laboratory research, clinical trials, research staff and graduate trainees, making the timing of federal payments critical to institutions that operate on narrow financial margins. The NIH’s pace of committing money to projects slowed sharply after President Donald Trump took office in 2025. In fiscal year 2025, the agency ran about 44 days behind its average obligation pace from 2021 through 2024. Through early July 2026, it was about 42 days behind that earlier benchmark. By that point, roughly three-quarters of the fiscal year had passed, but the agency had obligated only about half its budget. Jennifer Troyer, who led extramural operations at the NIH’s National Human Genome Research Institute before resigning at the end of 2025, said grants that had completed peer review were being subjected to additional scrutiny by the Department of Health and Human Services, the Office of Management and Budget or the White House. She described an unfamiliar grant status as a “black hole” where awards could remain stalled after the normal review process. Staffing reductions worsened the delays: At the institute where Troyer worked, the number of grants-management specialists fell from 11, plus two assistants, to three specialists. The consequences are particularly serious for multiyear grants, which are typically renewed annually. Before the current administration, renewals generally arrived slightly ahead of schedule to prevent interruptions. Renewals arriving at least 90 days late occurred in 3.9% of cases in fiscal year 2025 and 2.7% in fiscal year 2026, compared with 0.7% annually from 2021 through 2024. Ryan Gutenkunst, a molecular and cellular biology professor at the University of Arizona, said a delayed renewal forced him to consider which employees he might have to cut. His university provided temporary bridge funding, and the grant was renewed about two and a half months later. But institutions often limit such assistance to 90 days, leaving researchers vulnerable when delays last longer. The problem has affected districts represented by both parties. In Democratic congressional districts, grant renewals shifted from arriving an average of 3.4 days early to arriving 8.4 days late. In Republican districts, the change was from 3.8 days early to eight days late. Funding priorities have also changed. Spending on research focused on racial and ethnic minority health fell by more than $1 billion in 2025 compared with 2024, a 29% decline. At the same time, machine learning and artificial intelligence research received $468 million more, while networking and information technology gained $368 million. The shifts follow administration directives targeting what officials describe as wasteful or politically driven diversity, equity and inclusion programs. Researchers have reported that grants containing terms such as “climate change,” “DEI,” “gender” and “vaccine hesitancy” were flagged for review. Troyer said about half of the awards moving through her former institute had to be renegotiated, including changes to titles, abstracts and research aims. Mariana Stern, a professor at the University of Southern California’s Keck School of Medicine, said her research center dropped “Health Equity” from its name and became the CaRE2 Health Center. She said researchers have also had to revise how they describe their work. Other laboratories have faced direct financial losses. Scarlett Lin Gomez, who leads the Greater Bay Area Cancer Registry at the University of California, San Francisco, said its National Cancer Institute funding fell from $5.4 million in 2024 to $4.4 million in 2025 and $3.7 million in 2026. Gomez said she laid off about seven of roughly 50 employees last year and expects to eliminate another five or six positions this year. Researchers warn that delayed training grants could make academic careers less attractive to students already weighing higher pay and greater stability in the private sector. Stern said more students are choosing industry because they see the financial strain facing their mentors. Gomez described the trend as an “academic brain drain” that could accelerate under the current funding environment. Administration officials defend the changes. Emily Hilliard, a spokesperson for the Department of Health and Human Services, said the NIH’s Unified Funding Strategy is intended to promote transparency, rigorous science and evidence-based research. She said institute and center directors retain responsibility for final funding decisions after weighing multiple factors, as they have under longstanding grant practices. Ian Banks, science and development director at the Foundation for American Innovation and a White House science policy adviser, said the NIH has needed significant reform. He argued that the agency should examine whether its grantmaking system can be made more efficient, noting that researchers already spend a large share of their time on administrative work. Gutenkunst said reform is a legitimate subject for public debate, but decisions should not be driven by undisclosed word lists or made without scientists and the public. Researchers are particularly concerned about a proposed White House budget rule that could give political appointees greater authority over federal grant awards. Congress has preserved NIH funding in successive budget bills, and court cases have restored some money. Yet researchers say stable appropriations do not guarantee stable science: When grants arrive late or are redirected, labs can lose staff, experiments can become unusable and patients enrolled in clinical studies may face uncertainty. The long-term effects will depend not only on how much money Congress provides, but also on who controls its distribution and how openly those decisions are made.