Starting in late January, President Trump suspended two programs that provide American aid to international nuclear inspectors, potentially undermining his own goal of preventing Iran from developing a nuclear arsenal.

Though one of the programs has since been restored, the outcome of the actions has been to weaken confidence in an effort that for decades has exposed Iran’s strides toward the production of nuclear weapons. Some experts now worry that the disruptions will scare away talented professionals from the field of nuclear nonproliferation and hinder the global fight against the spread of nuclear arms.

Overall, the freezes have thrown uncertainty and confusion into programs that have had bipartisan support for decades. And now, for the first time, the people relying on global teamwork have to contend with the possibility that other vital collaborations may be discontinued or come under fire.

“These are disastrous policies,” said Terry C. Wallace Jr., a former director of Los Alamos nuclear laboratory in New Mexico. “They go against science and partnerships that lift a nation.”

The specific pauses in aid, and their partial reversals, were described by current and former U.S. government nuclear experts who spoke on the condition of anonymity for fear of reprisals.

The inspection unit of the International Atomic Energy Agency, which is part of the United Nations and based in Vienna, has long received aid from Washington to help it block, counter and respond to a wide range of global nuclear threats. Recently, at four sites in Iran, the team’s sleuths found traces of highly processed uranium, raising new questions around whether Tehran harbors a clandestine nuclear program to make atomic bombs.

Hours after taking office, Mr. Trump signed an executive order that halted U.S. foreign aid programs for a 90-day assessment that could lead to their restructuring or termination. Most notably, the freeze has upended humanitarian programs that fight disease and hunger in developing countries.

But the U.S. government nuclear experts said the president’s order also suspended aid from Energy Department labs that support the I.A.E.A. inspector corps. The two frozen programs recruit atomic inspectors, train them, supply them with equipment, teach them advanced methods of environmental sampling and use sophisticated lab devices to examine the samples they gather for clues.

Overall, the two programs act as intermediaries. They connect the Vienna detectives, who inspect nuclear sites around the globe as part of the I.A.E.A’s Department of Safeguards, to America’s network of nuclear labs, including Los Alamos. In essence, they direct world-class expertise and technical aid to Vienna — or did until Mr. Trump cut off foreign aid.

Both American programs, though located at Energy Department labs, are funded by the State Department.

The I.A.E.A. declined to comment on the aid interruptions, as did federal officials. In a statement, the State Department said the Trump administration makes U.S. national security a top priority.

“For that reason,” it added, “certain U.S. assistance to programs that support International Atomic Energy Agency efforts and capabilities to inspect nuclear facilities worldwide, including in Iran, are continuing. The work of the I.A.E.A. makes America and the world safer.” The statement said nothing about the atomic freezes and seemed to imply that some aid programs would be discontinued.

On Thursday, Wired magazine reported that the Pentagon was considering parallel moves. The magazine said documents it obtained showed that the Defense Department was weighing whether to slash the number of U.S. programs that work with global partners to curb the spread of chemical, biological and nuclear arms.

Countering Iran’s nuclear advances is among the Trump administration’s top foreign policy objectives. Secretary of State Marco Rubio said during his confirmation hearing in January that a nuclear-armed Iran “cannot be allowed under any circumstances.”

It’s unclear whether administration officials understand the depth of the relationship between the United States and the I.A.E.A. American aid helps the Vienna agency develop its inspector corps, whose staff, in turn, can go where American government experts may be unwelcome. The inspectors have exposed Iran’s hidden nuclear progress and helped the Eastern European nation of Moldova seize an illicit shipment of highly enriched uranium, which can fuel atomic bombs. It’s a two-way street.

In addition, the nuclear aid helps place American citizens in jobs at the Vienna agency. By statute, the I.A.E.A. promotes the peaceful uses of atomic energy, including nuclear reactors that light cities. It also has the responsibility to prevent those activities from being used surreptitiously to build atomic bombs.

U.S. programs that counter the global spread of weapons of mass destruction have grown steadily into a vast federal enterprise. The top players now include the departments of State, Energy, Defense and Homeland Security as well as the Nuclear Regulatory Commission, which trains people from more than 50 countries.

The programs have helped build supersensitive radiation detectors and promote the fight against atomic theft and sabotage. For this fiscal year alone, the National Nuclear Security Administration, an arm of the Energy Department, laid out a detailed plan to spend $2.5 billion on nuclear nonproliferation.

“These programs enhance U.S. security,” said Laura Holgate, a former American ambassador to the I.A.E.A. and a top adviser to President Barack Obama on nuclear terrorism. She added: “This is not charity. It’s in our self-interest.”

In recent decades, many Republicans have railed against the global nonproliferation apparatus, calling it bloated and ineffective. In April 2020, during his first presidential term, Mr. Trump proposed a budget that would have slashed funding for the Pentagon’s flagship effort to counter the spread of weapons of mass destruction.

Early in 2023, the Heritage Foundation published its “Mandate for Leadership,” a force behind its Project 2025 that many Trump loyalists helped write. The document called on the next administration to “end ineffective and counterproductive nonproliferation activities like those involving Iran and the United Nations.”

Mr. Trump’s executive order that halted U.S. foreign aid, signed on Jan. 20, made no direct mention of foreign nuclear aid suspension. And since then, with one exception, no lab directors or federal officials have alluded publicly to the freeze.

In late January, the freeze hit the recruiting program, which is based at Brookhaven National Laboratory on Long Island. Its International Safeguards Project Office not only signs up Americans to work as inspectors or associated personnel for the I.A.E.A., but also trains inspectors of all nationalities.

In addition, the program draws on the national lab network to devise inspection gear. Early on, it designed a hand-held device that became an I.A.E.A. favorite.

On Feb. 12, Kimberly Budil, director of Lawrence Livermore National Laboratory in California, referred to the Brookhaven freeze in a House hearing. She said a nonproliferation program in her lab set up through Brookhaven had been suspended pending Trump administration review.

“This is about a $1 million effort,” Dr. Budil told a House subcommittee on energy. “We don’t know if it will be restarted.” The press affairs office at the Livermore lab gave no substantive answers to repeated queries for details on the suspended aid.

As for the Brookhaven suspension, the lab’s office of press affairs; Raymond Diaz, the head of the lab’s International Safeguards Project Office; and the Energy Department declined to comment.

The second American program upended by the freeze is run by Oak Ridge National Laboratory in Tennessee. Unlike Brookhaven, it specializes in the use of sophisticated lab equipment to analyze swabs collected by I.A.E.A. inspectors for invisible traces of nuclear materials and readings that might point to illicit atomic work.

The Oak Ridge program is the U.S. intermediary for what the I.A.E.A. calls its Network of Analytical Laboratories, which it relies on to double-check and confirm its findings. Brian W. Ticknor, who runs the Oak Ridge program, declined to comment on the freeze, directing all questions to the State Department.

The current and former government nuclear experts said that the State Department reinstated the entire Oak Ridge lab program in late February. Similarly, they added, the Brookhaven program received a few waivers to resume work on specific efforts related to Iran, but most of its work and funding for other global nonproliferation programs remain on hold.

The experts said they expected that in the coming weeks, the full Brookhaven program would be unblocked. The current holdup at the State Department for approval of that step, they said, was now administrative rather than substantive.

The freeze reversals, they added, were rooted in Trump administration officials’ coming to see the importance of the I.A.E.A. in monitoring Iran’s secretive moves to make atomic bombs.