The union representing thousands of U.S. Environmental Protection Agency employees nationwide filed a lawsuit Tuesday over the EPA’s termination of their union contract last year, calling the move illegal.

The lawsuit against the EPA and its administrator, Lee Zeldin, was filed in U.S. District Court in Boston by the American Federation of Government Employees (AFGE) Council 238, which represents 8,000 workers nationally, as well as by AFGE Local 3428, which includes hundreds of the agency’s employees in Boston who cover New England.

The union contract had been agreed to in June of 2024, and wasn’t set to expire until 2028. But last March, President Donald Trump signed an executive order ending collective bargaining rights for employees at around 20 federal agencies, including the EPA. Following that order, the agency announced last August that it would terminate the collective bargaining agreement.

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“This was a long, hard-fought, fairly negotiated contract between the workers and management,” said Justin Chen, president of AFGE Council 238. “And to throw it all out with no regard to law, to any sort of statutory obligation, was a disgrace, quite frankly, with regards to the civil service and to the rule of law in this country.”

The EPA has not yet replied to GBH News’ request for comment.

“These career civil servants — they get into this kind of work because they believe in the mission and they believe in actually serving the public, especially when it concerns public health and environmental health,” Chen said. “So, with the reinstatement of our contract, we believe that we’ll be able to protect the rights of our workers, which will allow them to conduct their duties to their fullest capacities, and be able to provide the services that the American public deserves.”

The lawsuit filed Tuesday notes that the terminated contract had included “an important new first-of-its-kind ‘scientific integrity’ provision, which prevents the agency from retaliating against scientists whose findings differ from the political aims of the current president and protects a core value of the EPA that policy follows the science and not vice versa.”

The termination of that contract means EPA employees fear being fired for doing their jobs correctly, said Lilly Simmons, president of AFGE Local 3428, which represents EPA employees in New England.

“For example, you go out and you do some water sampling and it’s bad news, and you need to share that bad news, and you need to make sure that people are not using that water as a source of drinking water. But are you going lose your job for saying so?” Simmons asked. “That is a real concern for people. If they get something that management doesn’t like, will they be able to continue their work?”

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The EPA is involved in handling a number of issues increasingly important to New England, Chen noted, including flooding, erosion and issues like data centers that are impacting energy use.

“And the inability for an agency like the EPA to be honest and actually take seriously the concerns of people in New England is a disaster. And it will continue to be a disaster,” Chen added. “The inability of EPA workers to be able to speak up on this issue and actually give real practical advice and to be able to do the kind of work that’s necessary to protect the people of New England, you know, it’s tragic. And it doesn’t have to be this way.”

The executive order ending collective bargaining rights for the EPA cited national security concerns.

“This is obviously completely upside down,” Chen said. “When you don’t have the ability to go out and be protected in your speech with regards to concerns that you have a subject matter expertise in, the only people that lose — and will get hurt by this — is the American public.”

Last summer, about 140 EPA employees were put on administrative leave after they signed a letter of dissent, objecting to the administration’s targeting of the agency, a new focus on deregulation and what they described as the EPA’s disregard for scientific expertise. Ultimately, over 100 were given a two-week unpaid suspension and 15 were fired including one in the EPA’s Boston office.

“These workers did absolutely nothing wrong, nothing illegal, nothing untoward, essentially,” Chen said. “But EPA management followed through regardless with these illegal disciplinary actions against these workers. Had our collective bargaining agreement been in place, we would have been able to protect these people.”