Which federal programs and agencies were most affected by the 2025 shutdown?
Executive summary
The 43-day 2025 shutdown furloughed roughly 900,000 federal employees and forced about 2 million to work without pay, withholding nearly 3 million civilian paychecks worth an estimated $14 billion by the time funding returned on Nov. 12 [1] [2]. Critical frontline functions — notably the Transportation Security Administration, parts of the Department of Defense and core health programs such as Medicare and Medicaid — continued operating, while agencies that rely on annual discretionary appropriations (EPA, OSHA, many HHS programs, NNSA, FAA, National Parks and others) saw large furloughs, service disruptions and delayed data releases [1] [3] [2] [4] [5].
1. Who bore the brunt: agencies funded by discretionary appropriations
The shutdown hit hardest those agencies that depend on annual discretionary spending because their work stops when appropriations lapse. Agencies including the Environmental Protection Agency, many components of Health and Human Services, parts of the Department of Education and the Department of Commerce experienced broad furloughs and service interruptions under contingency plans [6] [3]. OSHA and the Farm Service Agency, for example, furloughed the majority of their workforces under their plans — OSHA furloughing roughly 72% of staff and FSA about 67% — halting routine inspections and farmer services [2].
2. Frontline exceptions: defense, TSA and entitlement programs continued
Not all programs shut down. The Department of Defense and the Transportation Security Administration continued core operations during the shutdown, as did entitlement programs such as Medicare and Medicaid, which kept paying benefits even where customer service and enrollment processes slowed because staff were furloughed [1] [7]. Those continuations masked disruption: air-traffic control capacity and airport operations were still impaired by staffing shortages among controllers and backups, forcing cancellations and reduced schedules [8] [5].
3. Large-scale workforce toll: pay, furloughs and morale
The human cost was immediate and quantifiable: nearly 3 million withheld paychecks representing about $14 billion in missing wages by the time appropriations were passed on Nov. 12 [2]. Roughly 900,000 federal employees were furloughed and millions more worked without pay during the lapse [1]. Surveys and reporting captured a drop in morale and long-term effects on retention: a Federal News Network survey found about 43% of its federal respondents reconsidered staying in public service because of the shutdown’s stresses [9].
4. Mission-critical but understaffed: NNSA, FAA and data gaps
Some agencies with safety-critical missions did remain partially operational yet at reduced capacity. The National Nuclear Security Administration furloughed the majority of its workforce for the first time in a shutdown, leaving less than a quarter of staff on mission-critical work [4]. The Federal Aviation Administration reduced traffic capacity, contributing to cancellations and a slow ramp back to normal; economists warned permanent data gaps — including possible loss of October employment and CPI releases — from suspended statistical reporting [8] [5].
5. Services to the public: parks, consumer protection and school feeding
Public-facing services were visibly affected: national parks and visitor centers closed, some federal consumer-protection offices (like the FTC) went offline, and school and food assistance saw interruptions — although USDA later released some funds, state agencies and school districts reported reimbursement delays [3] [1]. Head Start grants were explicitly threatened: HHS warned more than 58,600 children in 134 centers would be at risk of losing grants if the shutdown continued [1].
6. Political and policy consequences: backpay, RIF reversals and limits
The legislative deal that ended the shutdown restored back pay for furloughed workers, reversed thousands of layoffs issued during the lapse and put a short-term continuing resolution in place through Jan. 30 [5] [6]. The deal, however, left substantive policy fights unresolved (for example, expanded ACA subsidies), and agencies continue to face uncertainty over workforce reductions and reorganization efforts that predated the shutdown [6] [1].
Limitations and unanswered questions: available sources document which agencies and programs were heavily affected and give quantitative estimates of withheld pay and furloughs, but available sources do not mention a complete, line-by-line accounting of every program’s lost output or a final tally of permanent economic damage beyond the immediate $14 billion payroll figure [2] [5]. Competing perspectives exist within the coverage: some sources emphasize that safety-critical operations were preserved [1], while others stress serious capacity degradation even in those missions [8] [4].