Thousands of Health and Human Services (HHS) employees across the country are being dismissed on Tuesday as the Trump administration begins implementing its workforce-reduction plan, which could ultimately remove 10,000 staff members from the department through forced layoffs.

The job cuts mark the first tangible impact of the health secretary Robert F Kennedy Jr’s departmental overhaul announced last week, landing just days after Donald Trump moved to strip collective-bargaining rights from workers at HHS and other federal agencies.

Health department workers lined up outside federal buildings in Washington DC and Maryland on Tuesday morning, some for hours, as they waited to find out whether they were still employed. At least one office employee waved their badge at the entry point to see whether a red or a green light would appear – indicating whether they still had a job or not.

One employee, who has been with the department for 20 years and was waiting in line to find out her fate, said her colleagues have known for some time that HHS would be a target under the Trump administration.

“It’s in Project 2025,” she said. “Basically since February they’ve been telling us we might be let go.”

In the early 2000s, the department was among several others to offer legal reductions of force through voluntary buy-outs and early retirement packages. This time has been different.

“We’re being led through a security line like you would if you were at TSA,” the HHS employee, who is a supervisor, said. “We have to take off our shoes, take out our laptops, and they have to check our badge to make sure we can swipe it, and then check our names against a list.”

Kennedy’s restructuring goal is meant to dramatically reshape the department that oversees the US’s food supply, monitors disease outbreaks, conducts critical medical research and administers health insurance for nearly half the country. He has also said he will create a new office – “the administration for a healthy America” – which is meant to absorb agencies controlling billions of dollars in funding that manage addiction services and community health centers.

When finished, the cuts are expected to reduce HHS staffing from 82,000 to 62,000 positions – slashing nearly a quarter of its workforce through a combination of layoffs and early retirement offers.

Union representatives were notified last Thursday that 8,000 to 10,000 employees would be terminated, with positions in human resources, procurement, finance and IT targeted. Jobs in “high cost regions” and those deemed “redundant or duplicative” would be prioritized for elimination, according to a reduction-of-force email seen by the Guardian.

The department has outlined specific job losses across a number of agencies, including 3,500 positions at the Food and Drug Administration (FDA), 2,400 at the Centers for Disease Control and Prevention (CDC), 1,200 at the National Institutes of Health (NIH) and 300 at the Centers for Medicare and Medicaid Services (CMS).

In Congress, former health and human services staffers confronted Republican lawmakers about huge department cuts and layoffs sweeping through the agency. The Indiana Republican senator Jim Banks told the former HHS budget analyst Mack Schroeder he “probably deserved” to lose his job “because you seem like a clown”, according to video footage shared by Schroeder.

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In a post on LinkedIn, the former CMS executive Karen Shields said one team was given a reduction-in-force notice that suggested they contact the former director of the office if they had a complaint. But that director died in December, Shields wrote.

“I knew her. This would have broken her heart,” she added.

Back in Washington, the HHS employee waiting in the security line outside her office building said she could not wrap her head around the motive behind the White House’s plan.

“We help vulnerable people, vulnerable communities,” she said. “We’re civil servants. We don’t work for political parties.”

“This is not fair. Normally they look at job series, performances, costs,” she added in between tears. “I don’t think that’s happening.”