Nicholas Enrich, USAID's acting assistant administrator for global health, in the seven-page memo shared with staff, and which was seen by Reuters, said "political leadership" had made it impossible to deliver lifesaving humanitarian assistance around the world.
The email contradicts assurances from Secretary of State Marco Rubio that such aid would continue despite President Donald Trump and billionaire Elon Musk's cost-cutting campaign.
Twenty minutes later, Enrich sent another email, which was also seen by Reuters, that he had "just received notification that I have been placed on administrative leave, effective immediately".
A source familiar with the matter said the decision to put Enrich on administrative leave was made on Wednesday, before he sent his email on the consequences of USAID's dismantling.
Spokespeople for the State Department and DOGE did not immediately respond to requests for comment.
Enrich did not respond to a query from Reuters.
The blocked USAID programs include efforts to help contain a deadly Ebola outbreak in Uganda that had killed two and infected 10, Enrich said in the memo seen by Reuters.
"This will no doubt result in preventable death, destabilisation, and threats to national security on a massive scale," Enrich wrote in the memo, which was dated February 28 and shared widely with staff in the global health division on Sunday.
The Trump administration announced last week that it was cancelling nearly 10,000 foreign aid grants and contracts worth almost $US60 billion ($A97 billion), ending about 90 per cent of USAID's global work.
The shuttering of USAID is part of an unprecedented downsizing of the federal government by Musk's so-called Department of Government Efficiency. The agency's sudden demise has thrown global humanitarian relief efforts into chaos.
In a separate memo seen by Reuters, Enrich estimated that a year-long pause in lifesaving aid from USAID would cause between 71,000 and 166,000 additional malaria deaths, a nearly 40 per cent increase; an increase of between 28 per cent and 32 per cent in tuberculosis cases worldwide; and up to 28,000 cases of emerging infectious diseases such as Ebola.
After Trump ordered all foreign aid frozen in January pending a review, Secretary of State Marco Rubio issued a temporary waiver for lifesaving assistance, such as essential medicines, food and shelter.
Since February 14, Enrich said, "zero lifesaving health activities" have been approved.
