Bethesda, Maryland – September 11, 2026
The National Institutes of Health signed a secret 10-year agreement with the Department of Defense in early August that could redirect billions of dollars of infectious disease research funding to Pentagon-controlled accounts, prompting sharp criticism from congressional lawmakers who say they were never notified.
The interagency memorandum of agreement, signed on August 4 and 5, 2026, authorizes the transfer of funds from the NIH's National Institute of Allergy and Infectious Diseases to the Office of the Assistant Secretary of War for Nuclear Deterrence, Chemical, and Biological Defense Policy and Programs. The agreement would allow the Department of Defense to develop therapeutics, diagnostics, and protective equipment against pandemic influenza, chemical, biological, radiological, and nuclear threats, and emerging infectious diseases.
The agreement was executed last month without public announcement or advance congressional notification. It came to light during a House Appropriations hearing on September 3, when Representative Rosa DeLauro, the ranking Democratic member, questioned NIH officials about the arrangement. NIH Director Jay Bhattacharya signed the memorandum on August 5, the day after Defense Department biodefense chief signed it.
NIH spokespersons have told reporters the partnership would occur on a project-by-project basis, with all research staying within the scope of NIH's mission. An NIH spokesperson told Nature that "this partnership will only take place on a project-by-project basis, and all research will be within the scope of NIH's mission. There is no blanket transfer of funds."
NIAID's Parallel Restructuring
The defense agreement arrives as NIAID has also proposed major internal reorganization of its clinical research infrastructure. In late August, the institute published a Federal Register notice seeking public comment on eliminating its Division of Clinical Research and several offices within it.
The DCR plays a central role in facilitating NIAID's clinical research programs both domestically and internationally. It provides oversight of intramural clinical research, program planning, regulatory monitoring and compliance, statistical consultation, and capacity building for clinical research. The comment period on the proposed reorganization runs September 14 through September 18, 2026.
The notice states the goal is to "better align with Presidential priorities" and reflect the institute's updated mission focus. It would realign clinical operations across multiple NIAID components rather than abolishing the function entirely.
Congressional and Scientific Backlash
Representative DeLauro, chair of the House Appropriations Labor, Health and Human Services, Education and Related Sciences Subcommittee, called the arrangement a secretive attempt to siphon research funds away from NIH. Senator Patty Murray, ranking member on the Senate Appropriations Committee, also raised concerns about the lack of transparency.
The Infectious Diseases Society of America and HIV Medicine Association separately warned that NIAID's research infrastructure is already destabilized by delayed grant renewals and proposed restructuring. Their joint statement in late August said changes of this magnitude deserve longer, meaningful input periods from researchers and community partners.
The agreement text states its purpose is to support "advanced development of medical countermeasures against pandemic influenza, chemical, biological, radiological, and nuclear threats, and emerging infectious diseases." It expires on September 30, 2036, but can be extended by mutual consent.
Implications for Global Health Research
The proposed changes intersect with broader shifts at NIH under the current administration. NIAID staff were directed earlier in 2026 to remove "biodefense" and "pandemic preparedness" language from research priority documents. The agency's new strategic vision refocuses on domestic infectious diseases affecting Americans rather than global pandemic preparedness.
Researchers have expressed concern that moving biodefense work outside NIAID could fragment an infrastructure built around peer review, scientific expertise, and long-term public health priorities. Analysis in Health Affairs this spring highlighted how decades of U.S. investment in international HIV and infectious disease research have generated scientific advances that also benefit Americans.
Funding for NIAID's infectious disease research has faced sustained pressure. The agency's budget has been flat or declining in real terms over recent years, and many of its research centers and top leadership positions have faced vacancies or uncertainty.
The agreement allows the Department of Defense to enter into contracts, grants, and cooperative agreements to develop medical countermeasures. NIH would coordinate on statements of work, estimated costs, and place orders to transfer funding prior to contract awards. The arrangement creates a 10-year pathway for NIH funding to support defense-directed research on pandemic and biodefense threats.
Sources: Nature, September 11, 2026. Science, September 2026. AVAC Global Health Watch Issue 85, September 11, 2026. Interagency Agreement Between U.S. Department of War and NIH, August 2026. Federal Register Notice of Public Hearing: NIAID Proposed Reorganization, August 31, 2026. House Appropriations Committee Hearing Transcript, September 3, 2026. MedPage Today, August 2026.
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