The Trump administration intends to terminate the United States’ financial support for Gavi, the organization that has helped purchase critical vaccines for children in developing countries, saving millions of lives over the past quarter century, and to significantly scale back support for efforts to combat malaria, one of the biggest killers globally.

The administration has decided to continue some key grants for medications to treat H.I.V. and tuberculosis, and food aid to countries facing civil wars and natural disasters.

Those decisions are included in a 281-page spreadsheet that the United States Agency for International Development sent to Congress Monday night, listing the foreign aid projects it plans to continue and to terminate. The New York Times obtained a copy of the spreadsheet and other documents describing the plans.

The documents provide a sweeping overview of the extraordinary scale of the administration’s retreat from a half-century-long effort to present the United States to the developing world as a compassionate ally and to lead the fight against infectious diseases that kill millions of people annually.

The cover letter details the skeletal remains of U.S.A.I.D. after the cuts, with most of its funding eliminated, and only 869 of more than 6,000 employees still on active duty.

In all, the administration has decided to continue 898 U.S.A.I.D. awards and to end 5,341, the letter says. It says the remaining programs are worth up to $78 billion. But only $8.3 billion of that is unobligated funds — money still available to disburse. Because that amount covers awards that run several years into the future, the figure suggests a massive reduction in the $40 billion that U.S.A.I.D. used to spend annually.

A spokesperson for the State Department, which now runs what is left of U.S.A.I.D., confirmed the terminations on the list were accurate and said that “each award terminated was reviewed individually for alignment with agency and administration priorities, and terminations were executed where Secretary Rubio determined the award was inconsistent with the national interest or agency policy priorities.”

The memo to Congress presents the plan for foreign assistance as a unilateral decision. However because spending on individual health programs such as H.I.V. or vaccination is congressionally allocated, it is not clear that the administration has legal power to end those programs. This issue is currently being litigated in multiple court challenges.

Among the programs terminated is funding for the United Nations Food and Agriculture Organization, which conducts surveillance for diseases that can be transmitted from animals to humans, including bird flu, in 49 countries. Some major programs to track and fight malaria, one of the world’s top killers of children, have also been ended.

Dr. Austin Demby, the health minister of Sierra Leone, which relies on Gavi’s support to help purchase vaccines, said he was “shocked and perturbed” by the decision to terminate U.S. funding and warned that the ramifications would be felt worldwide.

“This is not just a bureaucratic decision, there are children’s lives at stake, global health security will be at stake,” he said. “Supporting Gavi in Sierra Leone is not just a Sierra Leone issue, it’s something the region, the world, benefits from.”

In addition to trying to reach all children with routine immunizations, Sierra Leone is currently battling an mpox outbreak, for which Gavi has provided both vaccines and critical support to deliver them, he said.

“We hope the U.S. government will continue to be the global leader it always been — putting money in Gavi is not an expenditure, it’s an investment,” Dr. Demby said

Gavi is estimated to have saved the lives of 19 million children since it was set up 25 years ago. The United States contributes 13 percent of its budget.

The terminated grant to Gavi was worth $2.6 billion through 2030. Gavi was counting on a pledge made last year by President Joseph R. Biden Jr. for its next funding cycle.

New vaccines with the promise to save millions of lives in low-income countries, such as one to protect children from severe malaria and another to protect teenage girls against the virus that causes cervical cancer, have recently become available, and Gavi was expanding the portfolio of support it could give those countries.

The loss of U.S. funds will set back the organization’s ability to continue to provide its basic range of services — such as immunization for measles and polio — to a growing population of children in the poorest countries, let alone expand to include new vaccines.

By Gavi’s own estimate, the loss of U.S. support may mean 75 million children do not receive routine vaccinations in the next five years, with more than 1.2 million children dying as a result.

The U.S. has been among the top donors to the organization since its creation, and became the largest during the Covid-19 pandemic. While European countries have historically provided significant funding, many are now reducing foreign aid spending as they grapple with the change in U.S. policy on Ukraine and the U.S. demand that they increase their defense spending. Japan, another major Gavi donor, is struggling with a depreciating currency.

Dr. Sania Nishtar, Gavi’s chief executive, said that she hoped the Trump administration would reconsider the decision to end its support. Gavi’s work keeps people everywhere, including Americans, safe, she said. In addition to protecting individual children, vaccination reduces the possibility of large outbreaks. The organization maintains global stockpiles for vaccines against diseases such as Ebola and cholera, deploying them in rapid response efforts for epidemics.

Gavi’s structure requires countries to pay part of the cost of vaccines, with their share growing as income levels rise; middle-income countries are weaned from support.

Although the administration has repeatedly said publicly that its foreign assistance review process has been concluded, the information in the documents suggests that there is still some fluidity in which programs will survive. Staff members of one major malaria program that was terminated weeks ago, and which appears on the list of canceled projects sent to Congress, for example, were informed on Monday that it is being restored.

Nevertheless, cuts to malaria response are deep. While awards that fund the bulk purchase of bednets and malaria treatments have been preserved, many of the programs to deliver these and other malaria control efforts in individual countries such as Cameroon and Tanzania — among the most affected in the world — have been terminated. Some organizations with awards that have not been officially canceled have received no funds for more than two months, and have folded. Without them, there is no one to take treatments from ports to local clinics, or deliver them to children.

The memo says that 869 U.S.A.I.D. personnel were working as of last Friday, while 3,848 were on administrative leave and 1,602 are in the process of being laid off. Of 300 probationary employees who were initially fired, 270 have returned to work following a court order prohibiting their dismissal.

Doctors in West Texas are seeing measles patients whose illnesses have been complicated by an alternative therapy endorsed by vaccine skeptics including Robert F. Kennedy Jr., the health secretary.

Parents in Gaines County, Texas, the center of a raging measles outbreak, have increasingly turned to supplements and unproven treatments to protect their children, many of whom are unvaccinated, against the virus.

One of those supplements is cod liver oil containing vitamin A, which Mr. Kennedy has promoted as a near miraculous cure for measles. Physicians at Covenant Children’s Hospital in Lubbock, Texas, say they’ve now treated a handful of unvaccinated children who were given so much vitamin A that they had signs of liver damage.

Some of them had received unsafe doses of cod liver oil and other vitamin A supplements for several weeks in an attempt to prevent a measles infection, said Dr. Summer Davies, who cares for acutely ill children at the hospital.

“I had a patient that was only sick a couple of days, four or five days, but had been taking it for like three weeks,” Dr. Davies said.

While doctors sometimes administer high doses of vitamin A in a hospital to manage severe measles, experts do not recommend taking it without physician supervision. Vitamin A is not an effective way to prevent measles; however, two doses of the measles, mumps and rubella vaccine are about 97 percent effective.

At high doses, vitamin A can cause liver damage; dry, peeling skin; hair loss; and, in rare instances, seizures and coma. So far, doctors at West Texas hospitals have said they’ve seen patients with yellowed skin and high levels of liver enzymes in their bloodwork, both signs of a damaged liver.

Many of those patients had been in the hospital for a severe measles infection; doctors discovered the liver damage only after routine lab work.

As of Tuesday, the outbreak, which began in January, had spread to more than 320 people in Texas. Forty patients have been hospitalized, and one child has died.

In neighboring New Mexico counties, the virus has sickened 43 and hospitalized two. Seven confirmed cases in Oklahoma have also been linked to the outbreak.

Local doctors and health officials have become increasingly concerned about the growing popularity of unproven remedies for preventing and treating measles, which they fear is causing people to delay critical medical treatment and to reject vaccination, the only proven way to prevent a measles infection.

In Gaines County, alternative medicine has always been popular. Many in the area’s large Mennonite community, where most cases have been clustered, avoid interacting with the medical system and adhere to a long tradition of natural remedies.

Health officials said the recent popularity of vitamin A use for measles could be traced back to a Fox News interview with Mr. Kennedy, in which he said he had heard of “almost miraculous and instantaneous recovery” with treatments like cod liver oil, which he said was “the safest application of vitamin A.”

In an opinion essay for The Washington Post on Tuesday afternoon, Kevin Griffis, who was until last week the communications director at the Centers for Disease Control and Prevention, wrote that he had resigned in part because of Mr. Kennedy’s handling of the outbreak.

“In my final weeks at the C.D.C., I watched as career infectious-disease experts were tasked with spending precious hours searching medical literature in vain for data to support Kennedy’s preferred treatments,” Mr. Griffis wrote.

In the weeks after the Fox News interview, drugstores in West Texas struggled to keep vitamin A and cod liver oil supplements on their shelves. “I did not hear anything about vitamin A until he said it on television,” said Katherine Wells, the director of public health in Lubbock.

One local doctor — whom Mr. Kennedy named in the Fox News interview as one of the physicians who had told him “what is working on the ground”— opened a makeshift clinic in Gaines County and began doling out various treatments, including vitamin A supplements, to treat active measles cases and to prevent infection.

Dr. Davies said she suspected that a majority of the children she had treated had taken vitamin A supplements at home.

Experts say that vitamin A can play an important role in the “supportive care” that doctors provide to patients with severe measles infections.

It works by replenishing the bodily stores depleted by the virus, which bolsters the immune system, said Dr. William Schaffner, an infectious disease specialist at Vanderbilt University Medical Center.

In the hospital, physicians give only two doses of the vitamin to children with measles, usually over the course of two days, and “very carefully calibrate” the amounts depending on age and weight, he said.

Dr. Schaffner emphasized that it is not a miracle treatment for the virus, and that there is no antiviral medication for measles. And there is no credible evidence that vitamin A helps prevent infection in children in the United States, where vitamin A deficiencies are exceedingly rare.

In fact, giving children repeated, high doses of the vitamin is dangerous. Unlike other vitamins, which are flushed out of the body through urine, excess vitamin A accumulates in fat tissue, making it more likely to reach dangerous levels over time.

“That kind of preventative use I think is especially concerning,” said Dr. Lara Johnson, another doctor at the Lubbock hospital.

“When we have kids taking it for weeks and weeks, then you do potentially have a cumulative impact of the toxicity,” she added.

Dr. Johnson added that local physicians were particularly concerned about parents’ relying on over-the-counter supplements — whose labels don’t always accurately reflect the amount of vitamin they contain — and accepting dosage recommendations from unverified sources.