The Trump administration has dismissed the few remaining health officials who oversaw care for some of the world’s most vulnerable people: more than 500,000 children and more than 600,000 pregnant women with H.I.V. in low-income countries.

Expert teams that managed programs meant to prevent newborns from acquiring H.I.V. from their mothers and to provide treatment for infected children were eliminated last week in the chaotic reorganization of the Health and Human Services Department.

Some of the consequences of the dismissals are only now coming to light.

While it was known that some staff members devoted to H.I.V. prevention in other countries had been lost, The New York Times has learned that all such experts have now been terminated or are awaiting reassignment at the Centers for Disease Control and Prevention, the State Department and the U.S. Agency for International Development.

These maternal health programs are still funded by the President’s Emergency Plan For AIDS Relief, or PEPFAR. But without personnel to manage the initiatives or to disburse the money, it’s not clear how the work will continue.

The Health and Human Services Department did not respond to a request for comment.

“We hope this is not a sign that treating mothers and children is no longer important in PEPFAR, and that this is a mistake that can be corrected,” said a federal health official who spoke on condition of anonymity for fear of retaliation.

The stakes are high. Already in sub-Saharan Africa, a child under 15 dies of AIDS every seven minutes.

On Tuesday, a study in The Lancet estimated that suspending PEPFAR could lead to about one million new H.I.V. infections by 2030 and could lead to nearly 500,000 AIDS deaths among children and the orphaning of 2.8 million more.

After the nascent Trump administration froze all foreign aid, Secretary of State Marco Rubio issued a waiver permitting delivery of “core lifesaving medicine, medical services” and other activities funded by the United States.

A waiver specific to PEPFAR later explicitly continued support for programs meant to prevent mother-to-child transmission of H.I.V., and to provide treatment of infected women and children.

The paperwork allowing the aid to resume took weeks after the waiver was issued, and several organizations are only just beginning to receive federal funds required to run the programs.

“You can dismantle something very quickly, but now you’re trying to build it back up with a fraction of the staff and potentially 5 percent of the institutional knowledge,” said a federal official who wasn’t authorized to speak to the news media and requested anonymity.

All experts in pediatric H.I.V. were all let go in the gutting of U.S.A.I.D., leaving a single unit at the C.D.C. with the expertise to advise overseas programs. That team was lost in last week’s reorganization, along with another that handles disbursement of funds for 300 grants in more than 40 countries.

Given the State Department waiver, those layoffs came as surprise to the federal health workers and to the organizations that rely on them.

“We clearly understood that H.I.V. services for mothers and children would fall under” the waiver, said Dr. Anja Giphart, executive vice president of medical and scientific affairs at the Elizabeth Glaser Pediatric AIDS Foundation.

The foundation depends on the C.D.C. for about 60 percent of its budget. “We were totally blindsided that the whole unit at C.D.C. is being terminated,” she said.

The organization has been promised funds until September. But only a few people were authorized to use the payment system at the C.D.C.

“Everyone is scrambling now to figure out how to pay country teams and partners,” said a C.D.C. official who requested anonymity for fear of retaliation.

Other experts said that they were not surprised by the hollowing out of the C.D.C.’s H.I.V. teams despite the waiver.

“What we’ve seen is that there’s no rhyme and reason to any of the actions that the administration is taking,” said Jirair Ratevosian, who served as the chief of staff for PEPFAR in the Biden administration.

Care for children and pregnant women with H.I.V. is complex.

Infants need an H.I.V. test different from the one used for adults, and infected babies must take a separate set of medications. They succumb quickly to complications when treatment is interrupted.

“Especially when you think about children, time is of the essence,” Dr. Giphart said. “That seems to not really be taken into consideration with all these changes that are being made.”

In low-income countries, pregnant women with H.I.V. usually get treatment at prenatal clinics. Without treatment, one in three pregnant women may pass H.I.V. on to her baby.

Treatment decreases the risk of transmission to less than 1 percent. PEPFAR has prevented nearly eight million such infections in newborns since its inception, in 2003.

The foreign aid freeze imposed in January has resulted in shortages of pediatric H.I.V. drugs in many countries and the delayed delivery of a new H.I.V. drug treatment.

The C.D.C. experts who were let go had been helping low-income countries prepare for this transition, tracking stocks and helping to direct the medications to the places with the most urgent needs, said an official who spoke on condition of anonymity for fear of retaliation.

“This coordination is especially critical right now because we’re in a period of immense change,” the official said.