Overview

Federal Science Workforce and Research Funding Upheaval

Workforce Reductions

As the administration sought to reshape U.S. research and development, it substantially scaled back and restricted what science the country pursues and the workforce that runs the federal scientific enterprise. The Trump administration directed federal agencies to undertake plans for large-scale reductions in force as part of a sweeping plan to shrink the size of the U.S. government, with agency heads instructed to coordinate plans with the Department of Government Efficiency, the cost-cutting initiative led by Elon Musk. These formal layoffs came on top of around 10,000 people already leaving agencies under the administration's "Fork in the Road" offer and early retirement incentives.

The losses varied by agency but were severe across the board. NSF lost one-third of its staff since the start of the Trump administration, according to the president of the union representing agency employees. At least 2,145 high-ranking NASA employees accepted a separation incentive as part of the administration's push to shrink the federal employee headcount. Massive layoffs across HHS were widely expected to sharply curtail public health services and medical research. HHS's Office of the Assistant Secretary for Planning and Evaluation fell from roughly 150 employees to fewer than 50, while the Agency for Healthcare Research and Quality lost 111 of its roughly 300 staff in a single round of cuts. The Food and Drug Administration also lost more than 20 percent of its staff.

Grant Cancellations and Ideological Screening

In an unprecedented move, officials began terminating already-funded grants at NIH in February 2025, and later at NSF. In total, 5,844 NIH grants and 1,996 NSF grants were cancelled or suspended. The administration disproportionately cancelled or froze projects on topics it disfavored, such as misinformation, vaccine hesitancy, infectious diseases, and research on people from underrepresented ethnic and gender groups, which it characterized as discriminatory and unscientific.

The grant cancellations extended well beyond NIH and NSF. The administration terminated dozens of health research grants at the Agency for Healthcare Research and Quality, telling grantees it was shifting priorities to issues like the "overmedication of children" and autism, with cuts hitting multiyear awards that had already been indefinitely delayed. Many of the impacted grants supported junior researchers and innovative studies focused on patient care, and the funding delays forced layoffs and the shutdown of programs already underway. Litigation complicated but did not fully reverse the cancellations. Two lawsuits filed in Massachusetts — one led by the American Public Health Association and another by a coalition of sixteen states — challenged NIH grant cancellations that appeared to target research involving race or gender; many cancellations were reversed following those suits, but much of the funding remained in legal limbo.

The Indirect Cost Battle

A separate but related front opened over university overhead. In February 2025, NIH published guidance capping facility and administration costs — the overhead universities charge for utilities, lab space, equipment, and administrative support — at 15 percent of direct research costs, well below the 50 to 65 percent rates most research universities had individually negotiated. The cap would have stripped roughly $4 billion annually from the nation's research infrastructure. Other agencies followed: the Department of Energy announced a similar cap in April 2025 and NSF followed in May, even after a federal judge had ruled the NIH move illegal.

Courts blocked the policy at each agency. The First Circuit Court of Appeals unanimously concluded that NIH violated statutory law and the agency's own regulatory procedures when it issued a policy capping reimbursement rates at 15 percent for current and new grants. The administration ultimately failed to meet the Department of Justice's April 2026 deadline to petition the Supreme Court to review the ruling, leaving the court's original permanent injunction in effect. The episode nonetheless demonstrated the administration's sustained intention to restructure the financial relationship between federal agencies and research universities — a goal it has continued to pursue through its FY2027 budget proposal, which again includes a 15 percent cap.

Budget Proposals and Congressional Response

The administration's FY2026 budget proposal sought cuts totaling $44 billion, or 22 percent, across all agencies engaged in scientific research, including reductions to NSF of 57 percent, NIH of 41 percent, and NASA of 24 percent. The proposed cut to NASA would have been the biggest single-year reduction in the agency's history and would have brought its funding to the lowest level since 1961 when adjusted for inflation, according to the Planetary Society. Congress refused, largely holding nondefense research and development spending stable. Even so, agencies quietly reshaped their spending: although NSF and NIH ultimately spent much of their FY2025 budgets, they did so by paying off more multiyear grants and funding fewer new grants than usual, reducing support for new areas of inquiry. The administration's FY2027 budget request again seeks similarly sharp reductions, including an across-the-board cap on indirect costs.

Significance and Impact

Amid the workforce overhauls, federal science agencies appear to be bearing the brunt of the changes; workforce reductions, resource cuts, and plans to increase political influence in the grantmaking process are all leading to declines in scientific development and innovation, with effects that will be felt for decades to come, according to the Partnership for Public Service. During FY2025, science agencies obligated $112.6 billion in spending toward project grants — a 24 percent decrease in grant funding from science agencies since 2024, according to USASpending data.

The damage is not only financial. Institutional memory, scientific pipelines, and long-running research relationships take years to build and can be destroyed quickly. NSF staff reported that the White House was withholding $2.2 billion of the agency's FY2025 funds, while NASA employees warned that the agency was closing out funded missions, representing what they called a permanent loss in capability. The disruption of junior researchers and early-career scientists is particularly consequential: funding delays forced layoffs and the shutdown of programs already underway, interrupting career trajectories in ways not easily reversed by restored appropriations.

Reactions and Debate

Resistance emerged both inside and outside the agencies. Hundreds of employees at NSF and NASA signed protest letters objecting to policy changes since the start of the Trump administration, including workforce reductions and grant terminations, revealing major shifts inside the agencies only some of which had previously been reported. NSF employees sent their letter directly to House Science Democrats as an official whistleblower complaint to protect signers from retaliation. NIH employees issued their own dissent letter, known as the Bethesda Declaration, in June 2025.

Congressional Democrats raised sustained objections, while Republicans were more divided. In several cases, the administration's proposed cuts were similar to those Congress largely rejected in its final budget for FY2026. The courts provided the most consistent check: permanent injunctions at NIH, NSF, the Department of Defense, and the Department of Energy all blocked the overhead cap. Former officials from both parties also weighed in publicly; former NASA administrator and astronaut Mark Kelly warned that the administration was effectively showing "experienced scientists, engineers, managers" the door at NASA, according to reporting on a press conference by former federal science leaders.

Defenders of the administration's approach argued that federal research spending had grown without adequate accountability, that ideologically motivated grants had proliferated, and that university overhead rates were an inefficient use of public funds. The administration framed its actions as restoring merit-based science and eliminating waste. Critics of indirect cost payments had long argued that universities use the money to cover expenses unrelated to federally funded research, and the Trump administration had tried unsuccessfully during its first term to lower the rates. The difference in the second term was the breadth and speed of the attempt.

Outlook

The White House budget request proposed steep cuts to proposed spending levels for research and development at civilian agencies, at $46.8 billion for FY2026, compared to $73 billion in enacted spending during FY2025. The FY2027 proposal renews the same ambitions, suggesting the administration views the first round of reductions as a floor rather than a ceiling. Whether Congress again moderates those proposals remains to be seen; the FY2026 appropriations cycle showed that bipartisan resistance to science cuts is real, but it also demonstrated that agencies can reshape their portfolios significantly without statutory authority simply by delaying grants, shifting priorities, and reducing new awards.

The workforce losses are in many respects irreversible in the near term. Experienced scientists and program officers who left through buyouts or layoffs are unlikely to return en masse, and rebuilding institutional expertise takes years. The Partnership for Public Service characterized the situation as a "generational loss" — not something that can be turned on and off like a light switch, but rather the destruction of something invested in over fifty years, disappearing over the course of eighteen months. Litigation over specific grant terminations remains pending in some venues, with courts divided on whether claimants must pursue monetary relief through the Court of Federal Claims. The indirect cost question is settled as a legal matter for now but continues to animate budget negotiations. How much of the disrupted research can be recovered, and over what timeline, is one of the most consequential unresolved questions facing American science policy.