HHS government shutdown contingency plans: What to know

The federal government has shut down, as Congress and the Administration failed to agree on annual funding bills for federal agencies or on a continuing resolution that would keep the government open while they finalize the fiscal year 2026 funding bills. We anticipate that the Department of Health and Human Services and its agencies will follow the contingency plan released Sept. 29, which outlines department and agency activities that will continue through the shutdown period and those activities that will not continue during the lapse period. The plan also provides details about which federal employees will be retained or furloughed during the shutdown. A memo from the Office of Personnel Management provides details on how federal employees are impacted based on their employment status, including those who may receive reduction in force notices.  

Last week, IDSA and HIVMA communicated our concerns to Congress about the potential negative impacts of a shutdown and the additional federal workforce reductions threatened by the Administration in the event of a shutdown. We urged lawmakers to reach an agreement that would protect critical public health functions, access to care and research. We also urged them to take action to extend the current telehealth flexibilities to avoid disruptions in care and to extend the enhanced marketplace premium tax credits enacted in 2021 to prevent a sharp increase in marketplace premiums.  

Below is a summary of activities that would not continue and would continue in the event of a shutdown. It is still unclear what additional staff may be laid off, as threatened last week by the Administration, so those potential impacts are not included in this summary. 

HHS overall 

• According to the plan, 32,460 employees are expected to be furloughed (nearly half of the current 76,717 employees).  
• All non-exempt or non-excepted activities not funded through the annual appropriations process or that are not related to the safety of human life or protection of property will continue, and staff performing those activities will be furloughed. These activities include:  
  • Oversight of extramural research contracts and grants  
  • Processing FOIA requests and public inquiries  
  • Data collection, validation and analysis  
• In the event of new public health emergencies or natural disasters at home or abroad, the plan will be revised to ensure a range of experts are on staff to manage these potential threats.   

Centers for Disease Control and Prevention  

Activities that will continue 

• Responses to urgent disease outbreaks and continuing efforts to support select programs including the U.S. President’s Emergency Plan for AIDS Relief and the Vaccines for Children program  

Activities that will not continue 

• Guidance to state and local health departments on programs including opioid overdose prevention and HIV prevention  
• Communication to the public about important health-related information.  
• Analysis of surveillance data for reportable diseases 
• Ongoing applied public health research by agency scientists to improve prevention methods and investigation of risk factors  
• Response to public inquiries about public health matters   
• Critical year-end surveillance reports would be delayed 
• Grant funding announcements would not be prepared, which will result in compressed times for applicants, such as state and local health departments and universities, to apply for funding 

National Institutes of Health 

Activities that will continue 

• Ongoing operations at the NIH Clinical Center to maintain the safety and continued care of its patients  
• Provision of basic services to protect the health of NIH animals and safeguard ongoing experiments or operations, and facilities and infrastructure 

Activities that will not continue 

• All NIH grant peer review meetings, advisory council meetings, issuance of new awards and program/grant management activities 
• Admission of new patients at the NIH Clinical Center (unless deemed medically necessary by the NIH Clinical Center director) 
• Initiation of new protocols at the NIH Clinical Center 
• Basic research conducted by NIH scientists 
• Translational research conducted by NIH scientists that develops clinical applications of scientific knowledge 
• Training of graduate students and postdoctoral fellows at NIH facilities 
• Scientific meetings at NIH facilities 
• Travel of NIH scientists to scientific meetings 
• Some NIH veterinary services 
• NIH scientific equipment services 
• Almost all NIH administrative functions, including the onboarding of non-excepted staff 
• Most NIH mail, cafeterias and visitor services 

Health Resources and Services Administration  

Activities that will continue 

• Activities funded through mandatory funding, advance appropriations, prior year carry-over funds and user fees, including the Health Centers Program, Ryan White – Parts A and B, the National Health Service Corps and the Teaching Health Center Graduate Medical Education program 

Activities that will not continue 

• • Vaccine Injury Program 
  • IT and administrative contracts  
  • Drafting and posting of FY 2026 Notices of Funding Opportunities and the review of applications for discretionary funded programs  
  • Limited ability to staff activities related to certain litigation 
  • Limited staff to support programs in maternal health, health workforce and behavioral health 

About IDSA and HIVMA 

The Infectious Diseases Society of America is a global community of 13,000 clinicians, scientists and public health experts working together to solve humanity’s smallest and greatest challenges, from tiny microbes to global outbreaks. Rooted in science, committed to health equity and driven by curiosity, our compassionate and knowledgeable members safeguard the health of individuals, our communities and the world by advancing the treatment and prevention of infectious diseases. Within IDSA, the HIV Medicine Association is a community of health care professionals who advance a comprehensive and humane response to the HIV pandemic, informed by science and social justice. Visit idsociety.org and hivma.org to learn more.