A highly regarded federal scientist filed a whistleblower complaint Wednesday against the U.S. Department of Agriculture (USDA), charging that he was punished for publicizing research showing a link between pesticides and the decline in bees and other pollinators.

Jonathan Lundgren, a USDA entomologist in Brookings, S.D., said in civil service documents that while the agency did not stop publication of the research, supervisors harassed him, tried to stop him from speaking out, and interfered with new projects.

His complaint caps months of speculation among beekeepers and other scientists who have been following his case. It was filed within the federal civil service system with support by Public Employees for Environmental Responsibility (PEER), a national nonprofit that defends government scientists on controversial environmental issues.

“We think the USDA is reflecting complaints from corporate stakeholders,” said Jeff Ruch, the group’s executive director. “This research is drawing consternation, which flows down the USDA chain of command to the researchers doing the work.”

Officials from the Agricultural Research Service, the USDA branch where Lundgren works, declined to answer questions about the case. In a prepared statement, spokesman Christopher Bentley said the agency is committed to scientific integrity.

“The USDA has implemented a strong scientific integrity policy to promote a culture of excellence and transparency,” he said. “That includes procedures for staff to report any perceived interference with their work, seek resolution, and receive protection … for doing so.”

Jonathan Lundgren, a USDA entomologist in Brookings S.D.

Lundgren is just one of many USDA scientists and employees who have come to PEER with similar complaints about harassment related to pesticide and pollinator research, Ruch said. But, he added, so far Lundgren is the only one willing to go public.

Lundgren’s decision was applauded by beekeepers, who long have regarded him as a leading scientific voice on the risks of the class of insecticides called neonicotinoids, which have been implicated in the decline of honeybees and other insects.

Steve Ellis, a Minnesota beekeeper who has been on the forefront of the neonicotinoid fight, said he was glad to see the USDA “called out on the rug.”

Other scientists have publicly expressed concern about scientific integrity at the agency where Lundgren works. This month, a co-researcher came to his defense in a published research paper, saying in a postscript that the agency had forced Lundgren to remove his name from it.

“I believe this action raises a serious question concerning policy neutrality toward scientific inquiry,” wrote Scott Fausti, a professor at South Dakota State University.

Lundgren did not respond to a request for an interview, but Ruch said he has been fighting with the research service internally for two years.

“His going public was a last resort,” he said. “He’s at the brink of professional elimination.”

Ruch said that Lundgren, an 11-year veteran of the agency, was highly regarded until 2014, when he published a research paper showing that neonicotinoids were harmful to monarch butterflies.

According to Lundgren’s complaint, his supervisor angrily confronted him about publishing a paper about a “sensitive” issue without permission. In the following weeks, he was widely quoted in the news media about the role of neonicotinoids in the decline of insects, and he was an external reviewer on a report on the same issue published by the Center for Food Safety, an advocacy group.

That was when “improper reprisal, interference and hindrance of my research and career began in earnest,” he said in his complaint. His supervisors pressured him not to talk to the media anymore, and weeks later they launched an investigation into him for “unprofessional behavior.”

His supervisors also thwarted new research projects, and harassed him about minor things like using an outside e-mail account and travel documentation.

A year ago, Lundgren filed a complaint with the USDA, charging that it was violating its scientific integrity policy, but the complaint was not upheld internally. Last August, he was suspended for two weeks without pay.

But a letter from one of Lundgren’s supervisors, also released by PEER, tells a different story of Lundgren’s case.

The letter said he was suspended because of a complaint by one of his lab employees, which triggered a five-month investigation, as well as falsification of travel charges, failure to follow supervisory instructions and other infractions.

His allegations of retaliation are unfounded, the letter said, and a two-week suspension was justified because he demonstrated “blatant disregard for agency rules and regulations.”

“Your continuing to engage in misconduct despite the imposition of previous disciplinary action suggest a low potential for rehabilitation,” the letter said.

Ruch said the whistleblower complaint will expose the internal record of Lundgren’s case to outside civil service scrutiny. It will produce internal agency documents, testimony from managers and employees, and require an evidentiary hearing before a panel of administrative judges.