Two weeks into President Trump’s sweeping freeze on foreign aid, H.I.V. groups abroad have not received any funding, jeopardizing the health of more than 20 million people, including 500,000 children. Subsequent waivers from the State Department have clarified that the work can continue, but the funds and legal paperwork to do so are still missing.

With the near closure of the American aid agency known as U.S.A.I.D. and its recall of officers posted abroad, there is little hope that the situation will resolve quickly, experts warned.

H.I.V. treatment and services were funded through the President’s Emergency Plan for AIDS Relief, or PEPFAR, a $7.5 billion program that was frozen along with all foreign aid on Mr. Trump’s first day in office.

Since its start in 2003 during the George W. Bush administration, PEPFAR has delivered lifesaving treatment to as many as 25 million people in 54 countries and had enjoyed bipartisan support. The program was due for a five-year reauthorization in 2023; it survived an effort by some House Republicans to end it and was renewed for one year.

Without treatment, millions of people with H.I.V. would be at risk of severe illness and premature death. The loss of treatment also threatens to reverse the dramatic progress made against H.I.V. in recent years and could spur the emergence of drug-resistant strains of H.I.V.; both outcomes could have a global impact, including in the United States.

The pause on aid and the stripping down of U.S.A.I.D. have delivered a “system shock,” said Christine Stegling, a deputy executive director at UNAIDS, the United Nations’ H.I.V. division.

“Now you need to see how you can work with the system as it is, to make sure that what is theoretically possible will actually happen,” she said.

On Jan. 28, Secretary of State Marco Rubio issued a waiver for lifesaving medicines and medical services, ostensibly allowing for the distribution of H.I.V. medicines. But the waiver did not name PEPFAR, leaving recipient organizations awaiting clarity.

On Sunday, another State Department waiver said more explicitly that it would cover H.I.V. testing and treatment as well as prevention and treatment of opportunistic infections such as tuberculosis, according to a memo viewed by The New York Times. The memo did not include H.I.V. prevention — except for pregnant and breastfeeding women — or support for orphaned and vulnerable children.

Although PEPFAR is funded by the State Department, roughly two-thirds of its grants are implemented through U.S.A.I.D. and the Centers for Disease Control and Prevention. Neither organization has released funds to grantees since the freeze was initiated.

In an interview with The Washington Post, Mr. Rubio appeared to blame the recipient organizations for not acting on the waiver, saying he had “real questions about the competence” of the groups. “I wonder whether they’re deliberately sabotaging it for purposes of making a political point,” he said.

But experts familiar with PEPFAR’s requirements said his comments belied the complexity of its system of approvals.

“The messaging and guidance from the State Department expose an ignorance of how these programs function — and an alarming lack of compassion for the millions of lives at risk,” said Jirair Ratevosian, who served as chief of staff for PEPFAR in the Biden administration.

For instance, the stop-work orders compelled each program to cease immediately. The organizations are now legally required to wait for equally explicit instructions and cannot proceed on the basis of a general memo, according to a senior official at a large global health organization that receives PEPFAR funds.

“We have to wait till we get individual letters on each project that tell us not only we can start work, but tell us which work we can start up and with how much money,” the official said. The official asked not to be named for fear of retaliation; 90 percent of the organization’s money comes from PEPFAR.

The freeze is also disrupting the network of smaller organizations that deliver H.I.V. treatment and services in low-income nations.

In a survey of 275 organizations in 11 sub-Saharan countries conducted over the past week, all reported that their programs or services had shut down or were turning people away, said Dr. Stellah Bosire, executive director of the Africa Center for Health Systems and Gender Justice.

At least 70 organizations reported disruptions in H.I.V. prevention, testing and treatment services, and 41 said that some programs had closed. “Without immediate intervention, these funding suspensions could lead to devastating reversals in public health progress,” Dr. Bosire said in an email.

In Kenya, 40,000 doctors, nurses and other health workers have been affected by the freeze, according to Mackenzie Knowles-Coursin, who was deputy chief of communications at the American mission in Nairobi until Monday. In South Africa, the halt in funding will affect the salaries of more than 15,000 health workers and operations across the country, the nation’s health minister, Aaron Motsoaledi, said during a televised news conference last week.

Some organizations rely on a patchwork of grants, with a stream of funding from one donor applied to purchasing medications and another stream applied to paying staff. Interruption of even one source can hobble the clinics, leaving them without medications to dispense or workers to dispense them.

The Uganda Key Populations Consortium, an umbrella organization that provides H.I.V. treatment and other services, has lost 70 percent of its funding. It has shuttered 30 of the 54 drop-in centers around the country that dispense medications, and it terminated the contracts of 28 of its 35 staff members.

The organization received about $200,000 per year from the C.D.C. via the Infectious Diseases Institute at Makerere University, as well as an $8 million grant over five years from U.S.A.I.D. The latter provided housing and employment assistance, including to gay and transgender people, and has been shut down to comply with Mr. Trump’s executive order on diversity, equity, inclusion and accessibility.

In 2023, Uganda enacted a sweeping law that criminalized consensual sex between same-sex adults and made same-sex relations while having H.I.V. punishable by death. It has caused scores of Ugandans to be evicted from homes and fired from jobs.

“Cases of human rights violations haven’t really slowed, and now it’s really concerning,” said Richard Lusimbo, director general of the Uganda Key Populations Consortium.

“We don’t even have the capacity or even the tools that we need to actually respond to some of these issues,” he said.

Some organizations dispense medicines to children, which requires more skill than treating adults. Children’s medications are tailored to their age, weight and prior exposure to antiretroviral drugs, and the children must be carefully monitored for drug resistance.

In children who acquired H.I.V. at birth, the infection can progress very quickly to illness, with death occurring as early as eight to 12 weeks after birth — shorter than the 90-day pause on foreign aid.

On Tuesday night, the Trump administration put nearly all of U.S.A.I.D.’s global work force on leave and recalled those posted abroad to return to the United States within 30 days.

“There’s a loss of institutional memory, which may be purposeful, but it’s also creating just a backlog of paperwork, and it’s paralyzing the whole system,” said Elisha Dunn-Georgiou, the president of Global Health Council, a membership organization of health groups.

“Who do you ask questions to?” she said. “How do you move to the next step?”

Without U.S.A.I.D. staff to process waiver applications, organizations fear they will not see funds anytime soon. Even large global health organizations are struggling to stay afloat; some have already cut programs and staff.

Even if the funds return quickly, it may not be easy to restart programs and return to something resembling normalcy, Ms. Dunn-Georgiou said.

“It costs a lot to restart something, so I don’t think we really know yet if that’s even possible,” she said.

Lynsey Chutel and Stephanie Nolen contributed reporting.