At the Veterans Affairs hospital in Pittsburgh, researchers spent months preparing for a clinical trial of a new drug to treat advanced cancers of the mouth, throat and voice box.

They were ready last month to start enrolling patients — veterans whose cancer had spread to other tissue and who had run out of treatment options.

Then a problem arose.

The hospital was unable to renew the job of a key staff member involved in running the study, a typically routine process thwarted by a hiring freeze imposed under the government-cutting project led by President Donald Trump and Elon Musk. Suddenly, the clinical trial was on hold.

“They were ready to enroll,” said Alanna Caffas, the CEO of the Veterans Health Foundation, which administers the trials. “They had the lab kits on site. They had the drug to dispense. But they couldn’t get the clinical research coordinator renewed.”

While Trump administration officials have promised to preserve core patient services, initial cuts at the VA have spawned chaotic ripple effects. They have disrupted studies involving patients awaiting experimental treatments, forced some facilities to fire support staff and created uncertainty amid the mass cancellation, and partial reinstatement, of hundreds of contracts targeted by Musk’s Department of Government Efficiency.

The changes have shaken the veterans department, which stands out in the labyrinth of agencies and offices under siege by Trump and Musk.

It is in many ways a natural target for reform — a bureaucratic behemoth with 480,000 employees, some 90,000 contracts and a documented history of scandals and waste.

But it also treats 9.1 million veterans, provides crucial medical research and, according to some studies, offers care that is comparable to or better than many private health systems. Even Project 2025, the conservative governing blueprint assembled by Trump allies, said the VA had transformed into “one of the most respected U.S. agencies.”

The VA is also one of the most politically sensitive departments in the government, serving a constituency courted heavily by Republicans, including Trump, who has made overhauling the agency a talking point since his 2016 campaign.

Now, with VA Secretary Doug Collins vowing a much deeper round of cuts — eliminating some 80,000 jobs and reviewing tens of thousands of contracts — some Republicans are warning that the tumultuous process risks undoing recent progress.

Republican lawmakers questioned Musk about the cuts during a closed-door meeting last week, with Sen. John Barrasso of Wyoming, the chamber’s No. 2 Republican, telling reporters afterward that, although improvements can be made, “we want to make sure veterans get the care they need.”

This account of the early days of DOGE-led cuts inside the VA is based on more than two dozen interviews with hospital administrators, current and recently terminated employees, heads of independent foundations that support the veterans’ health system, government contractors and research scientists. Many agreed to speak on the condition of anonymity because they want to continue to serve veterans or hope to be reinstated in their jobs, and feared retribution from the Trump administration.

Among the 2,400 employees fired from the VA since Trump’s inauguration are workers who purchase medical supplies, schedule appointments and arrange rides for patients to see their doctors. Many are veterans themselves. All were “probationary” employees, meaning they were relatively new on the job and had fewer legal protections. Some may be reinstated, pending court action.

James Stancil, an Army veteran who stocked supplies for emergency and spinal injury care at a VA hospital in Milwaukee, said he and nearly half his shift of supply technicians lost their jobs last month.

“If you double the work, I can guarantee you’re going to have wrong things and wrong stuff in the wrong place,” said Stancil, a member of the American Federation of Government Employees, whose role in his hiring paperwork was described as “critical.”

VA officials said the system is fully committed to serving its patients, insisting that no patients were affected by the cuts and that all savings would be reinvested in veterans.

“VA will always provide veterans, families, caregivers and survivors the health care and benefits they have earned,” the agency’s press secretary, Peter Kasperowicz, said in a statement. “But we’re also making major improvements to strengthen the department, including redirecting billions of dollars from nonmission-critical efforts to health care, benefits and services that directly support VA beneficiaries.”

A day after The New York Times asked about delays in clinical trials due to the hiring freeze, the veterans agency moved to address the problem facing research staffers like the ones in Pittsburgh, who are often paid by outside groups running the research but still need time-limited, unpaid appointments at the VA to work on site.

On Friday afternoon, the VA’s acting chief of research and development emailed employees saying that those with certain appointments set to expire soon will be given 90-day exemptions.

Collins appeared to bring some of his concerns about the agency’s future to a Cabinet meeting last week, asking Musk to be strategic in his government-shrinking process, the Times previously reported.

In public, however, Collins has expressed enthusiastic support for the effort. He has also exempted about 300,000 “mission critical” workers from being cut, including medical professionals like doctors and nurses.

“But we will be making major changes,” he said. “So get used to it.”

Trump’s Jan. 20 executive order freezing government hiring cut off many of the VA’s critical research staff midway through studies, said Rashi Romanoff, the chief executive of the National Association of Veterans’ Research and Education Foundations, which supports partnerships between the veterans department and nonprofits.

Romanoff estimated that some 200 research staff members involved in 300 or more trials were at risk of being cut off during the first 90 days following the federal hiring freeze, threatening to disrupt trials providing treatment to some 10,000 veterans if no action is taken. Scientists are already considering moving trials to other institutions, which will mean veterans are no longer first in line for participation, and could cause millions of dollars in research funds to go to waste, she said.