They handled the secure transport of nuclear materials — dangerous, demanding work that requires rigorous training. Four of them took the Trump administration’s offer of a buyout and left the National Nuclear Security Administration.

A half-dozen staff members left a unit in the agency that builds reactors for nuclear submarines.

And a biochemist and engineer who had recently joined the agency as head of the team that enforces safety and environmental standards at a Texas plant that assembles nuclear warheads was fired.

In the past six weeks, the agency, just one relatively small outpost in a federal workforce that President Donald Trump and his top adviser Elon Musk aim to drastically pare down, has lost a huge cadre of scientists, engineers, safety experts, project officers, accountants and lawyers — all in the midst of its most ambitious endeavors in a generation.

The nuclear agency, chronically understaffed but critically important, is the busiest it has been since the Cold War. It not only manages the nation’s 3,748 nuclear bombs and warheads, it is modernizing that arsenal — a $20-billion-a-year effort that will arm a new fleet of nuclear submarines, bomber jets and land-based missiles.

Since the last year of the first Trump administration, the agency has been desperately trying to build up its staff to handle the added workload. Though it was still hundreds of employees short of what it had said it needed, it had edged up to about 2,000 workers by January.

Now, with the Trump administration’s buyouts and firings, the agency’s trajectory has gone from one of painstaking growth to retraction.

More than 130 employees took the government’s offer of a payout to resign, according to internal agency documents obtained by The New York Times that have not previously been reported. Those departures, together with those of about 27 workers who were caught up in a mass firing and not rehired, wiped out most of the recent staffing gains.

Engaged in top-secret work, tucked away in the Energy Department, the agency typically stays below the public radar. But it has emerged as a headline example of how the Trump administration’s cuts, touted as a cure-all for supposed government extravagance and corruption, are threatening the muscle and bone of operations that involve national security or other missions at the very heart of the federal government’s responsibilities.

Risking taxpayer dollars

The exodus “is going to make the job more difficult because what you lost were some of your most valuable leaders,” said Scott Roecker, the vice president of the nuclear materials security program at the Nuclear Threat Initiative, a nonprofit organization. “These were very accomplished, very successful, very well-trained people who were performing complex, niche jobs.”

Among the departures: At least 27 engineers, 13 program or project analysts, 12 program or project managers, six budget analysts or accountants, five physicists or scientists, as well as attorneys, compliance officers and technologists, according to internal lists.

The agency lost not only officials deeply steeped in the weapons modernization program, but also a noted arms control expert at a time when Trump has said he hopes to restart talks with Russia and China about limiting nuclear arsenals.

“Here we are building new nuclear weapons, and they’re building nuclear weapons,” Trump said in the Oval Office last month. “We’re all spending a lot of money that we could be spending on other things.”

Ben Dietderich, the Department of Energy’s chief spokesperson, said, “Contrary to news reports, the Energy Department’s nuclear weapons production plants and nuclear laboratories are operated by federal contractors and have been exempt” from cuts.

But multiple current and former officials of the agency said the loss of staff would hobble the agency’s ability to monitor the more than 60,000 contract employees who carry out much of the agency’s work. That could encourage fraud or misuse of taxpayer dollars, rather than limit it, as Trump and Musk have vowed the new Department of Government Efficiency initiative will do.

“The federal oversight is vital,” said Corey Hinderstein, the agency’s deputy administrator for nonproliferation under President Joe Biden. “Do you have any construction projects at your house? You wouldn’t just say to the contractor: ‘I want something like this room. Have fun.’”

Andrea Woods, a spokesperson for the Energy Department, said in a statement, “NNSA is committed to continuing its critical national security mission through the development, modernization and stewardship of America’s nuclear deterrent and nonproliferation and counterterrorism efforts.”

The department has said that most of the fired employees handled administrative and clerical tasks that were not critical to the agency’s operation. But an analysis of the internal documents by the Times, coupled with interviews with 18 current and former agency officials, shows that is not true for the bulk of people who took the buyout.

Many who left held a top-secret security clearance, called Q, that gave them access to information about how nuclear weapons are designed, produced and used, officials said. The offer allowed them to go on administrative leave with pay through September, then resign.