Over all, the C.D.C.’s budget would be cut 17 percent. Dr. Thomas R. Frieden, who recently retired as the director of the C.D.C. and led its 2014 Ebola response, sent more than a dozen bullet points on Twitter last week cataloging how the proposed budget was “Unsafe at Any Level Of Enactment.”

Trump administration officials say they are trying to refocus scientific research in an era of domestic austerity. Too much federal science is competing with work that could be done in the private sector, they say. Under the president’s budget, the National Institutes of Health at large would be cut 18 percent. Within that, the National Institute of Allergy and Infectious Diseases, which handles Zika, Ebola and H.I.V./AIDS vaccine research, would lose 18 percent of its budget.

“The administration wholeheartedly believes in the commitment to research,” Mr. Mulvaney said Wednesday at the House budget hearing. “We’d like to see more focus on what they call basic research, which is research further away from the marketability of products because that is one of the gaps that the government can and should fill.”

The targeting is remarkably specific. At the N.I.H., the Fogarty International Center, a small program that in part trains foreign leaders in pandemic response, would be eliminated. Thousands of scientists and global health professionals rallied on Capitol Hill in April to protest the plan after a list of programs targeted for eradication was released.

“They’re making a very radical statement,” Dr. Morrison said. “The big picture is a movement toward suspicion of international programs. The administration is threatening to abandon multilateralism in a big way.”