Trump launches ‘DOGE’ Workforce Optimization Initiative executive order: What’s the impact on federal science agencies?

After establishing the “Department of Government Efficiency” last month, President Trump has announced a DOGE “Workforce Optimization Initiative” that could have ramifications for thousands of science and regulatory roles across agencies—from the National Science Foundation to the FDA. In particular, the new executive order aims to reform the federal workforce. Agencies are required to limit new career appointment hires to no more than one for every four employees that depart. This ratio is intended to curb workforce expansion except in areas related to public safety, immigration enforcement, or law enforcement.

In addition, the order states that each federal agency head must develop a hiring plan—in consultation with its DOGE Team Lead—that focuses on placing new hires in the areas of highest need. Agency heads will also be tasked with preparing to undertake potentially significant staff cuts in their workforce. This includes prioritizing the elimination of positions that perform functions not mandated by statute or law.

Finally, the order says agencies must submit reports identifying statutory requirements that mandate the existence of certain subcomponents, with an eye toward consolidating or eliminating redundant structures.

In a press briefing with President Trump, Elon Musk said such cuts were necessary, “We’ve got a $2 trillion deficit, and if we don’t do something about this deficit, [the country will go] bankrupt.” He added: “It’s not optional for us to reduce federal expenses. It’s essential for America to remain solvent as a country.” Musk said his goal was to cut the deficit in half.

Facing criticism that the DOGE-led cuts were draconian, Musk insisted that scrutinizing every expenditure is simply about ensuring that taxpayer dollars are spent in the public’s best interest. “It’s not draconian or radical,” he defended. When a reporter pressed him about potential conflicts of interest given his role as CEO of SpaceX—a company that has secured billions in federal contracts—Musk explained that he leaves the detailed filing to his teams, adding, for instance, “if you see any contract where it wasn’t by far the best value for money for the taxpayer, let me know, because every one of them was.”

The Musk-led approach to fiscal scrutiny is part of a broader push to reform government spending—a mandate that extends well beyond defense contracts and into scientific research.

National Science Foundation (NSF)

One of the hardest-hit entities under the new workforce optimization guidelines may be the National Science Foundation (NSF). Already facing cuts ranging from 25% to 50%, the mandated “one hire for every four departures” ratio could limit NSF’s scientific oversight capacity, posing fresh challenges to funding of thousands of university grants and fundamental research initiatives. Critics argue that such cuts pose a serious threat to America’s global leadership in cutting-edge science, since NSF funds a significant portion of basic research across scientific domains. Before the proposed cuts, NSF has distributed approximately $10 billion in grants annually. The FY 2025 budget request to Congress was for $10.183 billion.

Many grants seem to be in jeopardy. Nature recently reported that roughly 10,000 existing grants were marked for potential cancellation given their inclusion of keywords like “women” and “people of color,” which are targeted in the Trump Administration rollback of DEI initiatives.

NASA

President Trump’s Department of Government Efficiency (DOGE) is set to examine NASA’s payment systems, according to SpaceNews, prompting fresh concerns about potential conflicts of interest given DOGE chief Elon Musk’s role as CEO of SpaceX. NASA Acting Administrator Janet Petro has assured that strict conflict-of-interest policies are in place, but several members of Congress have raised alarms. Representatives Zoe Lofgren and Valerie Foushee, ranking members of the House Science Committee and its space subcommittee, sent a letter to Petro expressing concerns about Musk’s potential access to proprietary data. Meanwhile, Rep. Grace Meng, ranking member of the House Appropriations subcommittee that funds NASA, has urged the agency to revoke access for Musk and his staff. The examination of NASA payments comes amid broader uncertainty for the agency, including potential changes to the Artemis program and Boeing’s announcement of hundreds of planned layoffs related to Space Launch System work.

Department of Energy (DOE) National Laboratories

The Department of Energy operates numerous national labs, each critical to the nation’s research in fields ranging from advanced materials to nuclear physics. Analysts have raised alarms that large-scale reductions in force could force labs to drastically scale back or suspend major projects. According to a recent Politico report, directors of these labs are scrambling to identify which positions might be exempted under “national security” concerns, while bracing for substantial layoffs in areas not explicitly shielded by the executive order. While the order does not single out DOE or its labs by name, the mandate to shrink agency workforces and budgets extends to research programs that fund the labs. Direct reports related to DOGE-based cuts are, however, limited at the moment. If DOE’s Office of Science (the primary funder of many national labs) faces a budget cut in the range of 30%—as NOAA’s research arm is expecting (See: Science Agencies Brace for Mass Layoffs – AIP.ORG)—labs like Oak Ridge, Lawrence Berkeley, and Argonne would be forced to significantly curtail their activities. The Tri-City Herald based in Kennewick, Washington state noted that hundreds of federal workers were in fear for their jobs at a DOE Hanford office with a $3 billion annual budget. “It’s clear that some government labs, like other federal agencies, are suspending DEI programs. Physics World reported that Fermilab, the particle physics site, is pulling back on DEI programs. Early indications also suggest that climate science is likely to be cut as well, as Physics World has reported.”

A report from The Guardian revealed a backtrack at the National Nuclear Security Administration (NNSA). The NNSA, responsible for overseeing the US nuclear weapons arsenal within the Department of Energy, reportedly fired probationary employees as part of the initial cost-cutting measures. Yet officials soon realized these workers were essential, especially given the agency’s ongoing nuclear weapon modernization programs and the need to maintain the safety and reliability of the nuclear stockpile. As The Guardian reported, the agency resorted to asking supervisors to use personal emails to reach out to the dismissed workers and rescind their termination letters.

Food and Drug Administration (FDA)

Regulatory agencies are also bracing for the impact of the Workforce Optimization Initiative, with the FDA standing out as a key focal point. Some worry that fewer staff and resources could prolong review times for new drugs and devices, delaying patient access to lifesaving treatments. Endpoints News warns that the agency’s “non-mission-critical” programs might see immediate cuts. In general, FDA’s parent, the Department of Health and Human Services, is likely to see large-scale cuts. Early reports indicated that “thousands” of jobs could be eliminated at HHS agencies including FDA.

National Oceanic and Atmospheric Administration (NOAA)

Although NOAA focuses primarily on weather monitoring and environmental research, the agency also funds climate and oceanographic studies. If the DOGE-led reductions prioritize essential positions, the fate of long-term research programs—especially those not statutorily mandated—may be uncertain. Early signs from NOAA’s public statements suggest potential staff downsizing in areas such as coastal resilience and ocean exploration, heightening concerns about data gaps in climate science. CBS News reported that staff cuts in the ballpark of 50% were likely together with a 30% reduction in budgets. Project 2025, a policy blueprint by conservative think tanks that Trump has disavowed, proposed refocusing DOE national labs on nuclear deterrence and defense while scaling back climate and renewable energy research.

National Institutes of Health (NIH)

Though not singled out in the executive order itself, the NIH is closely watching the unfolding changes. Many fear that the attrition-driven hiring freeze could trickle down to NIH offices and programs deemed non-essential. Scientists interviewed by AAAS note that any slowdown in NIH grant processing or review cycles could stunt biomedical innovation, training opportunities for young researchers, and ongoing clinical trials designed to combat chronic and infectious diseases.

Environmental Protection Agency (EPA)

While the EPA’s core enforcement roles may be considered “public safety” functions, various programs—such as those related to climate, air quality monitoring, and environmental justice—may not be mandated by law in a strict sense. As a result, EPA subcomponents focused on research and policy analysis risk deeper cuts. Environmental advocates warn that this could weaken the agency’s ability to gather data on pollution trends or to guide states in managing environmental health hazards, as Southern Environment has noted.

Additionally, the Office of Personnel Management has introduced a Voluntary Buyout Program under which employees can receive incentives reportedly up to eight months of pay and benefits. Approximately 75,000 federal employees chose to opt in, although a temporary legal challenge briefly led to an extension of the sign-up deadline. Those who accepted are now in the process of separating from federal service. Meanwhile, revised guidance also highlights that probationary employees “can now be fired for simply being probationary,” making them especially susceptible to layoffs (See: NASA Watch). Federal unions are calling the scale of these downsizing moves “unprecedented,” warning that it amounts to a “pressure campaign to push workers out” and an attempt to “dismantle the federal government through mass firings.”

NASA

NASA Acting Administrator Janet Petro: recently noted that the agency “intends to comply” with the Workforce Optimization EO and is awaiting further guidance. She noted that Department of Government Efficiency personnel are now “onsite at the agency” to “start reviewing our contracts to find efficiencies.” She added that the Deferred Resignation Program opt-in is closed; NASA has begun implementation, notifying participating employees, according to NASA Watch.

Below is a summary table of reported workforce and budget impacts for several science-focused agencies, based on available public reporting:

Agency	Reported Layoffs / Staffing Cuts	Budget & Hiring Impacts	Programs & Projects Affected
NASA	“Hundreds” accepted buyout offers; probationary staff targeted; e.g., all recent hires at NASA’s Ames center, according to NASA Watch.	Spending review by DOGE in progress; 1-for-4 hiring rule in effect (See: Arnold & Porter).	Artemis Moon Program / SLS rocket workforce under scrutiny; potential conflict-of-interest concerns over Musk’s access to data.
National Science Foundation (NSF)	Planning for 25–50% staff layoffs, as AIP.org and others have noted.	Potential budget cut from ~$9B down to approximately $3B; 1-for-4 hiring limit.	About10,000 research grants flagged for cancellation, esp. DEI-related. Threat to US basic research leadership.
DOE National Labs	Large-scale RIFs expected; labs seeking to exempt “national security” staff, as Politico has noted.	30% cut rumored for DOE Office of Science parallel to NOAA’s 30% target. Hiring freeze in effect.	Labs may suspend major experiments, reduce user facilities; climate & clean-energy research at risk. Many labs halting DEI programs, as Physics World has noted.
NOAA	50% staff reduction rumored; employees told to brace for half cut, according to CBS.	Roughly 30% budget cut expected (AIP.org); possible agency reorganization to Interior Dept. under discussion.	Long-term climate and ocean research at risk if not mandated by law; coastal resilience, ocean exploration projects face cutbacks.
NIH	About 1,500 laid off (8% of workforce) on Feb. 14, focused on probationary hires. More cuts possible as HHS restructures, as SDPB/NPR reported.	“Thousands” of positions could be eliminated across HHS. Hiring freeze in effect. Clinical care roles possibly spared, according to SDPB/NPR.	Grant reviews, research support slowed; training programs disrupted. “Indirect costs” to universities under scrutiny, might be slashed.
CDC	About 1,300 employees (10% of staff) laid off; entire first-year EIS class cut (SDPB/NPR).	Operations impacted; uncertain future budget. Outbreak response capacity weakened with fewer “disease detectives.”	EIS, epidemic surveillance programs heavily affected; potential slower reaction to new public health threats.
FDA	No official count yet, but “thousands” at HHS level; FDA among those targeted.	“Non-mission-critical” programs on the chopping block; likely slower drug and device approval times (Endpoints).	Research, compliance, and outreach staff may be cut first. Core safety functions to remain but under strain.
EPA	Significant RIFs likely, focusing on roles not tied to statutory mandates.	Budget reduced for climate, research, and EJ initiatives; new hiring minimal.	Climate/air quality programs not classed as “public safety” could vanish; reduced environmental monitoring & data collection.

 

Other agencies impacted

Outside of these major science agencies, similar federal workforce reductions are affecting the U.S. Geological Survey (USGS), USDA’s research arms, USAID, the Consumer Financial Protection Bureau (CFPB), and the National Institute of Standards and Technology (NIST). USGS may see climate and geological research scaled back if deemed non-essential. USDA Research could lose funding for sustainable farming or nutrition projects. USAID is undergoing a partial merger with the State Department, prompting layoffs and lawsuits. CFPB has announced mass firings of probationary staff. NIST may face workforce reductions in its measurement science and manufacturing partnership programs. Federal employee unions such as AFGE and NTEU have flagged these cuts as damaging to American innovation and consumer protections.

Responses and emerging policy debates

Administration’s Stance (a “Necessary Pain” Approach): President Trump and DOGE chief Elon Musk frame the cuts as a fiscal imperative. Musk refers to them as “essential for solvency,” while also emphasizing that Heritage Foundation-linked proposals like Project 2025 are partially guiding a focus on dismantling perceived waste. They insist everything is about “best value for the taxpayer.”

Agency leadership reactions: Officials like NASA’s Janet Petro have tried balancing compliance with morale, while Sen. Angela Alsobrooks pressed newly confirmed HHS Secretary RFK Jr. on his stated intent to “clean house” at NIH. Some leadership figures have AAAS-backed concerns that losing senior scientists will harm the nation’s research enterprise long-term.

Lawmakers and legislative action: Representatives Zoe Lofgren, Valerie Foushee, and Grace Meng have voiced alarm over NASA conflict-of-interest issues, NIH staff losses, and NSF grant cancellations. Meanwhile, Sen. Angela Alsobrooks signaled potential hearings on deep workforce cuts. Some members of Congress see the layoffs as an overreach that bypasses normal appropriations authority, but others support the measures as budget discipline.

Union lawsuit and “Dismantling” concerns: Federal employee unions—AFGE, NTEU, and others—filed suit challenging the executive order as an unconstitutional end-run around Congress, describing it as an attempt at “dismantling the federal government through mass firings”. They point to the “unprecedented” scale of these moves and label them a “pressure campaign” to force resignations and buyouts. The Southern Environmental Law Center has warned these actions specifically undermine environmental enforcement, while other legal experts question whether Congress intended to fund agencies that lay off staff en masse.

External Analysts and Experts: Public health voices like Dr. Katelyn Jetelina and Dr. Georges Benjamin (APHA) warn of future crises if CDC capacity is eroded; Dr. Tom Frieden, former CDC director, calls the cuts “catastrophic.” Nicol Turner Lee of Brookings warns that removing government experts fosters a deeper reliance on contractors. Dan Ives of Wedbush Securities notes investor anxiety over Musk’s time splits. Russell Vought, a former Trump budget director, has championed deeper NIH and NSF cuts to curb “leftward agendas.”

Outlook: “Schedule F 2.0,” privatization

Potential shift to privatization: As agencies lose scientific expertise, some analysts predict more reliance on private contractors. Elon Musk has suggested private industry is more efficient; critics fear vital federal research programs will simply vanish or become less transparent under profit-driven contractors.

Schedule F 2.0 and Chilling Effect: Newly reclassified “policy-influencing” roles—often dubbed “Schedule F 2.0”—are easier to fire. This threatens career scientists working on controversial topics like climate change or DEI. Many staff report self-censorship to avoid scrutiny, worried about retaliation if they speak openly.

Legal and Legislative Unknowns: Courts will decide if the unions’ lawsuit can halt or reverse the layoffs. Congress could intervene through appropriations or by revoking certain executive authorities, but partisan divides may complicate swift action. In the meantime, agencies are implementing cuts, and the long-term consequences for U.S. research capacity, public health readiness, and environmental safeguards remain uncertain.

Beyond these agencies, other parts of the federal government face similar pressures. Broader contextual reports point to potential cuts in entities like USGS, USDA Research Arms, USAID (amid a merger with the State Department), CFPB, and NIST. As a result of the cuts, there could be a potential shift toward privatization and outsourcing and greater reliance on contractors. Meanwhile, new civil service rules (See this executive order for more details) are making it easier to fire policy-related positions..