More than three years ago, a small group of government scientists came forward with disturbing allegations.

During President Donald Trump’s administration, they said, their managers at the Environmental Protection Agency began pressuring them to make new chemicals they were vetting seem safer than they really were. They were encouraged to delete evidence of chemicals’ harms, including cancer, miscarriage and neurological problems, from their reports — and in some cases, they said, their managers deleted the information themselves.

After the scientists pushed back, they received negative performance reviews and three of them were removed from their positions in the EPA’s division of new chemicals and reassigned to jobs elsewhere in the agency.

On Wednesday, the EPA inspector general announced that it had found that some of the treatment experienced by three of those scientists — Martin Phillips, Sarah Gallagher and William Irwin — amounted to retaliation.

Three reports issued by the inspector general confirmed that the scientists’ negative performance reviews as well as a reassignment and the denial of an award that can be used for cash or time off were retaliatory. They also detailed personal attacks by supervisors, who called them “stupid,” “piranhas” and “pot-stirrers.”

The reports called on the EPA to take “appropriate corrective action” in response to the findings. In one case, the inspector general noted that supervisors who violate the Whistleblower Protection Act should be suspended for at least three days.

The reports focus only on the retaliation claims. The inspector general is expected to issue reports in the future about the whistleblowers’ scientific allegations.

In an email sent to the staff of the Office of Chemical Safety and Pollution Prevention after the reports were released, EPA Assistant Administrator Michal Freedhoff wrote that the office plans to hold a “refresher training on both scientific integrity and the Whistleblower Protection Act” for all managers in the office. Freedhoff also wrote that the office is “reviewing the reports to determine whether additional action may be necessary.”

In a statement to ProPublica, the EPA tied the problems laid out in the report to Trump. “The events covered by these reports began during the previous administration when the political leadership placed intense pressure on both career managers and scientists in EPA’s new chemicals program to more quickly review and approve new chemicals,” the agency wrote, going on to add that the “work environment has been transformed under Administrator Michael Regan’s leadership.”

Trump campaign spokespeople did not immediately respond to requests for comment.

A second Trump presidency could see more far-reaching interference with the agency’s scientific work. Project 2025, the radical conservative policy plan to overhaul the government, would make it much easier to fire scientists who raised concerns about industry influence.

“I’m worried about the future because there are groups out there pushing for changes to the civil service that would make it so I could be fired and replaced with a non-scientist,” said Phillips, a chemist. Publicly available versions of the inspector general’s reports redacted the names of all EPA employees, including the scientists, but Phillips, Gallagher and Irwin confirmed that the investigations focused on their complaints.

Phillips said the experience of having his work changed, facing hostility from his supervisors and agonizing about whether and how to alert authorities was traumatic. He began pushing back against the pressure from his bosses in 2019, trying to explain why his calculations were correct and refusing their requests to change his findings, he said.

In one case, someone had deleted a report he had written that noted that a chemical caused miscarriages and birth defects in rats and replaced it with another report that omitted this critical information. After Phillips asked that the original report be restored, he was removed from his position within the EPA’s division of new chemicals and assigned a job elsewhere in the agency.

“I was turned into a pariah,” Phillips told ProPublica about the almost yearlong period when he was sparring with his managers in the new chemical’s division. “I lost sleep. I dreaded going to work. I was worried every time I had to meet with my supervisor or other members of the team. It made me question whether I wanted to continue in my job.”

He and the other scientists said they felt vindicated by the inspector general’s findings.

“It’s gratifying and a relief,” said Irwin, who has worked at the EPA for 15 years.

Irwin, who has a doctorate in biochemistry and molecular biology and three board certifications in toxicology, was transferred from the new chemicals division into a division of the agency he calls “existing chemicals,” after refusing to change several reports, including one on a chemical that he suspected of causing reproductive, immune and neurological problems. Irwin said his supervisor later cited his refusal to sign off on that assessment as a reason to downgrade his rating in his annual performance review.

The division where Irwin and the other scientists worked plays a critical role within the EPA. Companies that develop new chemicals are required to get permission from the EPA to introduce them to the market. If the agency finds that they could pose an unreasonable risk to health or the environment, it must, by law, regulate them, which can involve limiting or forbidding their production or use.

Irwin feels he is particularly suited to the work on new chemicals. “I have a strong ability to look at a chemical and pick out what its toxicity would be based on the structure.” When he was transferred, he said, “I got put on something I didn’t want to do.”

After they were forced to leave their jobs assessing new chemicals, the scientists filed the first of what would be six complaints with the EPA inspector general in June 2021. Their allegations, which detailed industry pressure that continued under the administration of President Joe Biden and pointed fingers at career officials who still worked for the EPA, were the subject of a 10-part series I published in The Intercept. Three of those career scientists named in the complaints subsequently left the EPA. And the agency ordered changes to address the corruption the whistleblowers had alleged, including the creation of two internal science policy advisory councils aimed at shoring up scientific integrity.

“These whistleblowers have been beaten down, ostracized and punished, when all they were trying to do was to protect us,” said Kyla Bennett, director of science policy at Public Employees for Environmental Responsibility, an organization that helped the scientists draft the complaints to the EPA inspector general.

The inspector general’s reports said supervisors defended their actions, claiming that the whistleblowers took an overly conservative approach in their assessments and that, in some cases, criticisms the supervisors had relayed from the companies that submitted the chemicals were valid. One supervisor said scientists “were expected to make compromises to complete the new chemicals assessments.”

The inspector general released two additional reports that did not substantiate allegations of retaliation made by two other scientists.

Bennett said she was particularly concerned about how the outcome of the upcoming presidential election could affect the whistleblowers. “If there is another Trump administration, I will be petrified for them,” she said.

If Trump fulfills even some of the promises made in Project 2025, job security for the whistleblowers — and all EPA scientists — will become much more tenuous. Project 2025 specifically calls for new chemicals to be approved quickly and proposes that all employees whose work touches on policy in federal agencies would become at-will workers, allowing them to be fired more easily.

Although Trump has attempted to distance himself from the effort, saying, “I don’t know what the hell it is,” reporting by ProPublica showed that 29 out of 36 speakers in Project 2025 training videos worked for him in some capacity.

All three scientists who were found to have been the victims of retaliation said they worry that the underlying problems they raised have not been adequately addressed and might worsen.

The scientists said they were still concerned about industry pressure on the EPA’s chemical approval process.

“It’s been four years since we first started raising concerns about what was happening, and we haven’t seen a resolution yet,” Gallagher said. “We haven’t gotten assurance that the concerns we’ve been raising will be fixed.”

Still, Gallagher said she thinks the inspector general’s investigation might begin to lessen the burdens she’s felt since she blew the whistle at the EPA. “I’m hoping that I’ll be able to feel valued in my job again,” she said.