Treating H.I.V. across dozens of nations. Stopping the forced labor of Chinese workers. Training Mexican and Colombian police in anti-narcotics enforcement.

Those are just a tiny sample of aid programs around the world operating with grant money from the U.S. government that could be permanently shut down under an executive order President Trump signed last week to halt foreign aid.

The sense of crisis among aid groups worldwide is surging, as American officials tell groups they must obey an almost universal stop-work order issued by Secretary of State Marco Rubio after Mr. Trump’s directive.

The officials say the groups must freeze nearly all programs that have received any of the $70 billion of annual aid budget approved by Congress through bipartisan negotiations. They include programs that provide medicine, shelter and clean water in dire conditions and often make the difference between life and death.

Uncertain of whether they can pay salaries or get any future funding, groups around the world said they are starting to lay off employees or furlough them. In the United States alone, tens of thousands of employees, many of whom live in the Washington area and rely on contract work with U.S. agencies, could lose their jobs. Some have already been laid off.

Leaders of aid groups say they have never seen such an expansive and damaging directive, even during periods of aid reassessment by earlier administrations. Many of them are scrambling to contact lawmakers and other U.S. officials to get urgent messages to Mr. Rubio. They said some programs will be hard to restart after a temporary shutdown, and many could disappear.

The State Department said the move was aimed at ensuring that all foreign aid programs “are efficient and consistent with U.S. foreign policy under the America First agenda.”

The crisis deepened on Monday evening, when Jason Gray, the acting head of the United States Agency for International Development, put about 60 top officials on paid leave. He wrote in an email that those officials had taken actions “designed to circumvent the president’s executive orders.” On Tuesday, office workers removed photographs of leaders from the walls. Contractors have also been fired or put on leave.

Mr. Rubio said in a cable to U.S. missions abroad that the halt would last at least through a 90-day assessment period. But U.S. officials have already told some aid groups that certain programs, including ones that promote diversity, women’s reproductive rights and climate resilience, will be permanently cut.

U.S. agencies will need to break contracts during the halt, and they will likely need to pay fees. Among the U.S.A.I.D. employees put on paid leave are three lawyers, including the lead ethics lawyer, according to one person briefed on the situation.

The executive order halting foreign aid was the president’s first major foreign policy action, and many aid groups are only now understanding its broad scope. Foreign assistance money generally supports humanitarian, development and security programs, and it makes up less than 1 percent of the government budget.

Two Democratic members of the House, Gregory Meeks of New York and Lois Frankel of Florida, sent Mr. Rubio a letter on Saturday saying that lives were being “placed at risk” because of the aid halt. “Congress has appropriated and cleared these funds for use, and it is our constitutional duty to make sure these funds are spent as directed,” they wrote.

The stop order applies to most military and security assistance programs, including in Ukraine, Taiwan and Jordan. Much of that aid is disbursed by the State Department. Military aid to Israel and Egypt is exempted, as is emergency food assistance.

Mr. Trump’s decision to halt foreign aid could cause long-term damage to U.S. strategic interests, critics of the action say. Policymakers from both parties have long regarded foreign aid as a potent form of American power, a way to increase U.S. influence overseas using a tiny budget compared with military spending. Many development programs support democracy, education and civil rights efforts.

In recent years, China has tried to win more global influence with development projects, and it could gain ground as the United States retreats.

“This 90-day stop-work is a gift to our enemies and competitors — with effects that go beyond the immediate harms to people,” said Dr. Atul Gawande, the assistant administrator at U.S.A.I.D. in the Biden administration.

“It trashes our alliances with scores of countries built over half a century, trashes our world-leading expertise and capacity and threatens our security,” he said.

Dr. Gawande noted that U.S.A.I.D. has the largest footprint abroad after the military, employing hundreds of thousands of contractors, who will now be dismissed or put on leave.

Some former officials say a goal of the action could be to dismantle U.S.A.I.D. and move its work to the State Department — while keeping the amount paltry. The Trump appointee at the State Department overseeing foreign aid is Pete Marocco, a divisive figure in the first Trump administration who worked at the Pentagon, State Department and U.S.A.I.D. At the aid agency, employees filed a 13-page dissent memo, accusing him of mismanagement. Senior State Department officials can exercise authority over U.S.A.I.D., though the agency usually operates autonomously.

Some of U.S.A.I.D.’s critical work is listed on its website. One document says that during the civil war in Sudan, a United Nations agency relied on U.S. government support to screen about 5.1 million children age 5 and under for malnutrition, and it provided about 288,000 children with lifesaving treatment last year between January and October.

Smaller groups will struggle to survive. China Labor Watch, a New York-based group with overseas offices that aims to end forced labor and trafficking of Chinese workers, is shutting down programs that rely on $900,000 of annual aid from the State Department, said Li Qiang, the organization’s founder. Seven staff employees will be placed on unpaid leave and could depart for good, Mr. Li said, adding that employees who lose their work visas might have to return to China, where they could be scrutinized by security officers.

Groups worldwide that have relied on U.S. funding are now “victims of this disruption, leading to distrust in the U.S. government,” he said.

He continued: “This will further isolate the U.S. internationally. Damaging national credibility and alienating allies for short-term gains will have lasting repercussions.”

The clampdown also cripples the President’s Emergency Plan for AIDS Relief, or PEPFAR, the celebrated program started by President George W. Bush that is credited with saving more than 25 million lives. A shutdown of the program would likely cost millions of lives in the coming years, health experts said. The program’s work involves more than 250,000 health workers in 54 countries.

“When the funding stops before the epidemic is under control, you erode the investments you’ve made in the past,” said Dr. Linda-Gail Bekker, who heads the Desmond Tutu H.I.V. Center at the University of Cape Town in South Africa.

Simultaneously, Mr. Trump’s decision to withdraw from the World Health Organization has prompted that group to tighten its belt, curtailing travel and limiting operations on the ground.

On Sunday night, employees of the Centers for Disease Control and Prevention were instructed to immediately stop communicating with W.H.O. staff. and other international partners.

The blackout means American officials are likely to lose access to information about human outbreaks, including of mpox, polio and the emerging mosquito-borne disease Oropouche, and animal diseases, like swine flu, that could devastate the nation’s agricultural industry, Dr. Gawande said.

U.S.A.I.D. has helped to contain 11 serious outbreaks of Ebola and other hemorrhagic fevers in the last four years. One such disease, Marburg, is smoldering even now in Tanzania, with 15 confirmed cases and eight probable cases. Ten people have died.

“This is a disease with no test, no treatment and no vaccine that’s been approved,” Dr. Gawande said.

On Monday, Trump administration officials instructed organizations abroad to stop distributing H.I.V. medications that were purchased with U.S. aid money, even if the drugs are already in clinics.

Separately, officials worldwide were told that PEPFAR’s data systems would be shut down on Monday evening and that they should “prioritize copying key documents and data,” according to an email viewed by The New York Times. The system was maintained by a contractor forced to stop work because of the aid freeze.

About 90 percent of Dr. Bekker’s work in South Africa is funded by PEPFAR and the National Institutes of Health. Her team has helped to test H.I.V. medications and preventive drugs, and vaccines for Covid and human papillomavirus, or HPV, all of which are used in the United States.

Shutting down PEPFAR, which accounts for 20 percent of South Africa’s H.I.V. budget, would add more than a half million new H.I.V. infections and more than 600,000 related deaths in the country over the next decade, Dr. Bekker and her colleagues have estimated. The effect is likely to be far worse in poorer countries, like Mozambique, where PEPFAR funds the bulk of H.I.V. programs.

Abruptly halting treatment can endanger patients’ lives, but it can also increase spread of the virus and lead to resistance to the available drugs.

The Trump administration’s actions will cause long-lasting harm, including to Americans, said Asia Russell, executive director of the advocacy group Health Gap.

“If you’re trying to achieve a review of all foreign assistance, including PEPFAR, you can do that without attacking the programs through stopping them,” Ms. Russell said.

“It’s extraordinarily dangerous and perhaps deadly to do it this way,” she said, “but it’s also wasteful and inefficient.”