Lifesaving health initiatives and medical research projects have shut down around the world in response to the Trump administration’s 90-day pause on foreign aid and stop-work orders.

In Uganda, the National Malaria Control Program has suspended spraying insecticide into village homes and ceased shipments of bed nets for distribution to pregnant women and young children, said Dr. Jimmy Opigo, the program’s director.

Medical supplies, including drugs to stop hemorrhages in pregnant women and rehydration salts that treat life-threatening diarrhea in toddlers, cannot reach villages in Zambia because the trucking companies transporting them were paid through a suspended supply project of the United States Agency for International Development, U.S.A.I.D.

Dozens of clinical trials in South Asia, Africa and Latin America have been suspended. Thousands of people enrolled in the studies have drugs, vaccines and medical devices in their bodies but no longer have access to continuing treatment or to the researchers who were supervising their care.

In interviews, more than 20 researchers and program managers described the upheaval in health systems in countries across the developing world. Most agreed to be interviewed on the condition that their names not be published, fearing that speaking to a reporter would jeopardize any possibility that their projects might be able to reopen.

Many of those interviewed broke down in tears as they described the rapid destruction of decades of work.

The programs that have frozen or folded over the past six days supported frontline care for infectious disease, providing treatments and preventive measures that help avert millions of deaths from AIDS, tuberculosis, malaria and other diseases. They also presented a compassionate, generous image of the United States in countries where China has increasingly competed for influence.

The State Department and U.S.A.I.D. did not respond to requests for comment.

There will now be no one to take custody of millions of dollars’ worth of supplies for vital oxygen systems, purchased for programs funded by U.S.A.I.D. that support health clinics in some of the world’s poorest countries. The shipments, now in transit, are scheduled to reach ports in the coming days, but employees of those programs have been ordered to stop work.

On Tuesday night, Secretary of State Marco Rubio issued an exemption to the funding freeze for “lifesaving humanitarian assistance,” including what a State Department memo called “core lifesaving medicine.” However, shuttered H.I.V. and tuberculosis treatment programs have been told by their contacts at U.S.A.I.D. that they cannot resume work until they receive written instruction that the waiver applies specifically to them.

Also on Tuesday, a federal judge blocked the freeze until Feb. 3. But in practice, most U.S.A.I.D. country offices and programs are proceeding as if the freeze remains in place.

They have been unable to obtain clarification on whether and when their work can continue because their assigned contacts at U.S.A.I.D. have either been fired or furloughed, or are under strict instructions to not talk to anyone.

Despite the court order, thousands of people have already lost their jobs as a result of the freeze. About 500 U.S.-based employees of U.S.A.I.D. were fired. In countries from India to Zimbabwe, staff members for health projects were immediately fired. An organization called the International Centre for Diarrhoeal Disease Research, Bangladesh, which does research on a top killer of children, laid off more than 1,000 employees this week.

If the waiver announced by Mr. Rubio does not apply to their work — as is likely because it is expected to exempt only a narrow scope of activities — many nonprofit groups will not have enough funds to pay their employees or maintain supplies. Already, organizations that rely on U.S.A.I.D. funds have not been able access any money, even for reimbursement of expenses already incurred.

Two-thirds of the staff of the President’s Malaria Initiative, an organization founded by former President George W. Bush that is the largest donor to anti-malaria programs and research worldwide, have been fired. Those employees were contract staff members, because the agency had longtime hiring freezes for permanent positions, and included some of the most senior and respected scientists working on malaria control in the world.

While the interruption of H.I.V. treatment has prompted an outcry, the suspension of malaria work also immediately jeopardizes lives, said a scientist who was a senior staff member at the President’s Malaria Initiative for a decade and was fired on Tuesday.

Malaria interventions in Africa are carefully planned around rainy seasons, the time of which varies by region. Houses are sprayed with insecticide, and children are treated with an antimalarial medication during peak malaria transmission times.

“You could open the funding floodgates again tomorrow and you will still have children dying months from now because of this pause,” the scientist said.

More than 50 million children received preventative drugs before the rainy season last year.

The delivery of rapid tests and malaria drugs into Myanmar, where cases of malaria increased nearly tenfold to 850,000 in 2023 (the most recent figures available) from 78,000 in 2019, has been frozen. Some organizations now have no workers left to distribute the supplies even if they were to arrive.

In some parts of the country, more than 40 percent of cases are of a type of malaria that is often deadly in children under the age of 5. Malaria drugs would seem to qualify under the stipulation of “lifesaving humanitarian assistance, including essential medicines” included in the waiver, but in the absence of certainty, no one has been bold enough to try to free the drugs now stuck at the Thai border.

Some 2.4 million anti-malaria bed nets are sitting in production facilities in Asia, manufactured to fulfill U.S.-funded orders and bound for countries across sub-Saharan Africa. Those contracts are now frozen, because the U.S.A.I.D. subcontractor that bought them is not allowed to talk to the manufacturer under the terms of the freeze. Contracts for eight million more nets are now in limbo, an executive with the manufacturer said.

U.S.A.I.D.’s largest project is called the global health supply chain, an effort to streamline procurement of supplies for H.I.V., malaria, maternal health and other key areas, to make the system more efficient and save money. It operates in more than 55 countries where, in many cases, it supplies the bulk of key medicines. Now its global web of staff has been ordered to stop work except for essential tasks, like guarding commodities in warehouses.

In Zambia, U.S.A.I.D. supports the bulk distribution of public health products, using the private trucking industry to move medicines from a central supply depot to seven regional hubs, from which they are taken by truck, motorbike and boat to rural health centers. It’s part of the extensive U.S. support of the health system in Zambia, one of the world’s poorest countries, and over time it has been working to build up the supply chain capacity of the government.

Since the stop-work order was issued last Saturday, all of the vehicles transporting health products have been stopped. “They have effectively paralyzed the Zambian public health sector by pulling out so abruptly,” said one consultant who worked with the program. Similar U.S.-funded systems, now frozen, also moved a major share of basic medical supplies in Mozambique, Nigeria, Malawi and Haiti.

In East Africa, medical researchers working on projects to find ways to stop transmission of H.I.V. and develop more effective contraception have found themselves floundering for explanations to give to participants in their clinical trials.

“We have women testing vaginal rings, they already have the rings in them, people who got an injectable for H.I.V. prevention — when you say ‘stop,’ what happens to them?” said an H.I.V. researcher who is an investigator on a number of clinical trials. “We have an ethical obligation to people who volunteer for trials.”

Apoorva Mandavilli contributed reporting.