The Department of Defense has signed an interagency agreement with the National Institutes of Health that would shift funding earmarked for infectious disease and biodefense research at the National Institute of Allergy and Infectious Diseases toward accounts controlled by the Office of the Assistant Secretary of War, according to congressional Democrats and reporting from Nature and Science magazine.
What the agreement does
The agreement facilitates the transfer of NIH funds to the Office of the Assistant Secretary of War and is set to run through 2036. It does not specify a dollar figure, but House Appropriations Committee ranking member Rosa DeLauro and Senate Appropriations Committee ranking member Patty Murray say the arrangement could move billions of dollars that Congress had already appropriated for NIAID’s infectious disease work. NIAID’s biodefense and emerging infectious disease portfolio accounts for roughly a third of the institute’s $6.6 billion annual budget.
The stated purpose, according to the text of the agreement, is to support development of medical countermeasures against pandemic influenza, chemical, biological, radiological, and nuclear threats, and emerging infectious diseases. NIH disclosed the arrangement only after Democrats on the House Appropriations Committee pressed the agency for information, according to the committee’s public statement.
NIAID’s clinical research division is also being reorganized
Separately, NIAID has proposed eliminating its Division of Clinical Research and redistributing its clinical operations and oversight functions across other components of the institute. The Federal Register notice, published August 31, 2026, describes the change as an effort to align the institute’s structure with updated priorities. NIAID opened a public comment period on the reorganization running from September 14 through September 18, 2026, with comments directed to NIAIDExecutiveServices@mail.nih.gov.
Lawmakers push back
DeLauro called the arrangement a secretive attempt to siphon research funds away from NIH, saying it diverts money intended to help Americans exposed to HIV, influenza, tuberculosis, and other infectious diseases. Murray raised similar objections in a statement from the Senate Appropriations Committee, characterizing the move as an effort by the Pentagon to draw on NIH funding for its own priorities. Both lawmakers argue the transfer circumvents the appropriations process Congress uses to direct how federal research dollars are spent.
Infectious disease researchers and public health specialists have also raised concerns, warning that redirecting money away from NIAID’s civilian infectious disease programs could set back ongoing work on diseases that primarily affect civilian populations rather than military ones. The Pentagon has faced budget pressure this year following an extended military engagement with Iran, which Democrats say is part of the context for the funding request.
What happens next
The interagency agreement is expected to be finalized by the end of September 2026, when the current fiscal year closes and some previously appropriated funds would otherwise expire. NIAID’s public comment period on the clinical research reorganization runs concurrently. Neither HHS nor the Department of Defense has publicly detailed the specific programs or dollar amounts that would be affected, and further scrutiny is expected from the House and Senate Appropriations Committees in the coming weeks.
Sources: Bloomberg Government, “Pentagon Is Redirecting NIH Research Funding, DeLauro Says” · Science, “Outrage greets NIH pact that could funnel biodefense research funds to Pentagon” · Nature, “Revealed: inside the US military’s plan to tap huge sums from the NIH” · House Committee on Appropriations, “Defense Officials Attempt to Raid NIH Funds to Cover Department of Defense Activities” · Federal Register, “Notice of Public Hearing: NIAID Proposed Reorganization”
