In recent years, the Food and Drug Administration hired experts in surgical robots and pioneers in artificial intelligence. It scooped up food chemists, lab-safety monitors and diabetes specialists who helped make needle pricks and test strips relics of the past.

Trying to keep up with breakneck advances in medical technology and the demands of a public troubled by additives like food dyes, the agency enticed scores of midcareer specialists with remote roles and the chance to make a difference in their fields.

In one weekend of mass firings across the F.D.A., much of that effort was gone. Most baffling to many were the firings of hundreds whose jobs were not funded by taxpayers. Their positions were financed through congressionally approved agreements that routed fees from the drug, medical device and tobacco industries to the agency.

Known as user fees, the money provides adequate staffing for reviews of myriad products. While criticized by some, including the nation’s new health secretary, Robert F. Kennedy Jr., as a corrupting force on the agency, the industry funds are also widely viewed as indispensable: They now account for nearly half of the agency’s $7.2 billion budget.

Though the F.D.A. is believed to have lost about 700 of its 18,000 employees, some cuts hit small teams so deeply that staff members believe the safety of some medical devices could be compromised.

Among the layoffs were scientists supported by the fees who monitor whether tests pick up ever-evolving pathogens, including those that cause bird flu and Covid. They hobbled teams that evaluate the safety of medical devices like surgical staplers, new systems for diabetes control and A.I. software programs that scan millions of M.R.I.s and other images to detect cancer beyond the human eye. The cuts also eliminated positions for employees who have played a role in assessing the brain-implant technology in Elon Musk’s Neuralink devices.

The layoffs affected so many key experts that a major medical device trade group has requested that the Trump administration reconsider the job cuts.

The dismissals also included lawyers who warned retailers about underage tobacco sales and scientists who studied the safety of e-cigarettes and new heat-not-burn devices. The tobacco division — which is fully funded by an excise tax on cigarettes — lost about 85 staff members.

Dr. Robert Califf, the F.D.A. commissioner under President Biden, said the personnel cutbacks seemed scattershot. Taking a not-so-subtle aim at Mr. Musk’s Department of Government Efficiency, which is reducing the federal work force, Dr. Califf said the layoffs were, in effect, “anti-efficiency.”

“These are not hires that are done arbitrarily,” he said. “They’re done to meet a need.”

A lawsuit challenging the firings filed by unions, including one that represents some F.D.A. employees, failed to stop the layoffs in a ruling issued Thursday. Other cutbacks reduced the 2,000-member staff of the F.D.A.’s food division, which is supported by tax dollars.

Jim Jones, the former director of the division who resigned on Monday over the cuts, said that he had briefed the Trump transition team on his efforts to create a new office that would review a premier target of Mr. Kennedy and his agenda to Make America Healthy Again: food additives that are already on the market.

Nine people from that food-chemical-safety staff of 30 are gone, including specialized toxicologists and chemists, Mr. Jones said in an interview.

“They’ve created a real pickle for themselves,” by cutting staff members working on a key priority, Mr. Jones said. “You just can’t do an assessment for free and you can’t ban chemicals by fiat.”

In interviews with 15 current and former agency staff members, they said those who were laid off had been probationary employees, a group that included agency veterans who took on new roles, were recently promoted or were hired in the last two years.

Those who remained said that they had been scrambling to pick up pressing medical device reviews and move forward with studies to bulletproof methods for detecting deadly bacteria during inspections at food production sites.

Divisions that review novel medications, vaccines and gene therapies were largely spared. Officials with the F.D.A.’s parent agency, the Department of Health and Human Services, did not respond to requests for comment.

The F.D.A. employees fired last weekend were notified in uniformly worded emails that their skills were not needed and that their performance was “not adequate to justify further employment by the agency.” Yet many of them said that their performance reviews had said they exceeded expectations.

Tony Maiorana, 37, a chemist, worked on product approval and safety in the fast-changing field of diabetes devices. In the last decade, the field has moved from painful needle pricks and test strips to systems that measure glucose levels just below the skin and automatically infuse the needed insulin.

The work of reviewing new products is painstaking: Novel algorithms measure and dispense insulin; materials implanted in the body must evade rejection by the immune system; and millions of patients from toddlers to the elderly are at risk if devices malfunction.

Still, about half of Dr. Maiorana’s product-review team was eliminated, he said.

“If you’re a patient and you complain, we are the ones that field your complaints,” he said. “We are the ones that monitor the death reports. We’re the ones that are telling companies: ‘Hey, there’s a big pattern of error happening here. People are dying or ending up in the hospital because of your device’ and ‘What has changed? What happened?’”

Dr. Maiorana said that he had expected his government job would be “chill,” but it turned out to be intense. His team had to assess whether studies of new devices that had never been used in humans were safe for adults and children. They also had to watch online marketplaces for diabetes technology that had not been approved by the agency.

“This is the reason the F.D.A. was founded — to protect the public,” Dr. Maiorana said.

Albert Yee, 59, an expert in biomechanics and robotics, was fired on Saturday. In his unit, four of 11 staff members, who review the safety of surgical robots, were let go.

Robotic surgery is increasingly employed in operating rooms across the country, used in cardiothoracic, gynecological and bariatric surgeries. Dr. Yee had worked in the industry and in academia before joining the F.D.A.

He said his team was highly specialized, including an expert with a doctorate in medical robotics and a physician who had conducted robotic operations.

He said that robotic devices had become so complex that the team’s diverse expertise was critical to evaluate not just the safety of such tools but also concerns about cybersecurity.

“All of these devices now — if they’re attached to the hospital network, they become an avenue to get into the hospital network or get into the device itself,” Dr. Yee said.

He said the team also fielded a flood of applications for surgical apparatus developed abroad that were similar to those made by companies based in the United States. He said the applications required close attention to catch problems that could endanger patients.

“The institutional knowledge we’re losing is just horrific,” he said. “I am concerned about public safety with this type of purge.”

Nathan Weidenhamer was a lead reviewer of cardiovascular devices and other high-risk implants.

He said he was shocked and disappointed to be laid off because he and other reviewers in the device division were partly funded by industry-generated fees.

“I naïvely thought we were important, critical public servants and I’d be spared,” he said.

The layoffs clearly did not skip over employee slots created and funded by the agreements negotiated with the industries, congressional lawmakers and F.D.A. officials. The industries provide billions of dollars in return for staff equipped to meet strict deadlines for decisions on product approvals — though not all go in companies’ favor. The money is also used to make the F.D.A. a competitive employer in specialized fields that require advanced degrees.

Some of the deadlines are viewed by F.D.A. staff members as demanding, particularly the 30-day clock requiring them to authorize or add comments to studies of devices that are being implanted in humans for the first time. If the agency does not respond within that time-frame, the study is given a green light under the law.

The depth of cuts to medical device staff prompted AdvaMed, a trade association for the industry, to push back in a letter to a top Health and Human Services official.

The letter detailed about 180 medical device staff cuts, which included 25 experts in artificial intelligence, a 20 percent reduction in biostatisticians who evaluated studies of novel devices and the loss of molecular biologists with expertise in diagnostic tests that pinpoint a cancer subtype. The firings also applied to a top official who was recently recruited to oversee about 10,000 product applications and meeting requests per year.

The group said it appreciated the Trump administration’s efforts to improve efficiency. But “they may have missed the mark on how they rolled it out,” Scott Whitaker, the president of AdvaMed, said in an interview.

Medical device companies benefit when the F.D.A. is well staffed with people who have the expertise to guide the safe development of new technology, he added.

“One that is slow and overregulates is not good,” he said. “One that is under-resourced and doesn’t regulate at all — that’s not good either.”

Alice Callahan contributed reporting.