Late last year, Jonathan Lundgren, a South Dakota-based entomologist with the U.S. Department of Agriculture, submitted an article to the scientific journal Naturwissenschaften. It described how clothianidin—one of a controversial class of pesticides called neonicotinoids—harmed monarch butterflies. The paper was accepted. Then, in February, a supervisor confronted Lundgren. She informed him that the paper shouldn't have been submitted without official approval. It was sensitive.

Not long after, the National Academy of Sciences scheduled Lundgren to give a presentation on the effects of genetically modified crops on farmland ecology. As is customary, the NAS would pay for his travel to Washington, D.C. Lundgren accepted, but didn't complete the requisite agency paperwork—something that's technically against the rules, but not unusual, with scientists instead filing when they return. Lundgren was reportedly boarding the plane when instructed to return home and reimburse airfare costs out of his own pocket.

In August the USDA formally suspended Lundgren for these transgressions. But according to Lundgren, he wasn't punished for breaking a few rules. Instead, he says, the very agency responsible for America's farms and food punished him for his science.

For anyone who cares about scientific integrity, or about agricultural practices and policies with profound consequences for everyday life, it's a disturbing allegation. The potential ramifications extend beyond Lundgren to other scientists who might be discouraged from studying important but politically contentious topics.

“There's a message: If you want to prosper at USDA, don't make waves,” says Jeff Ruch, the executive director of the watchdog group Public Employees for Environmental Responsibility. “When you do what Jonathan is doing, you do so at your own peril.”

On Wednesday, PEER filed a federal whistleblower complaint on Lundgren's behalf. According to his complaint, the suspension was part of a campaign of harassment that started last spring after two incidents. First, Lundgren talked to a journalist about the risks of a new genetic-engineering technique pioneered by the agribusiness-behemoth Monsanto. Then he peer-reviewed a report by the Center for Food Safety that criticized the overuse of neonicotinoids, which are ubiquitous in American agriculture and linked to widespread declines in pollinators.

After that, recounted Lundgren in a document released with his complaint, “improper reprisal, interference, and hindrance of my career began in earnest.” He was told not to speak again to the media about those topics. His human-resources department launched a six-month-long investigation of Lundgren's lab, interviewing his staff and reviewing their emails in a search for misconduct. Some were dismissed.

According to Lundgren, supervisors rejected his research proposals, throwing his grant-seeking efforts—the lifeblood of any lab—into disarray. A trip abroad to give a presentation became a red-tape nightmare; slides in the presentation, he was told, needed to be reviewed by at least seven administrators, none with direct expertise in his research. Under the strain he stepped down as lead scientist on a major project at his facility, the North Central Agricultural Research Laboratory.

Lundgren was even asked to remove his name as co-author from an article, “The causes and unintended consequences of a paradigm shift in corn production practices,” in the journal Environmental Science and Policy. “I believe this action raises a serious question concerning policy neutrality toward scientific inquiry,” wrote his co-author, the economist Scott Fausti of South Dakota State University, in a footnote to the paper.

Of course, it’s not yet clear what actually happened. Maybe Lundgren just didn’t get along with his boss. It happens. Asked for comment, the USDA declined to discuss Lundgren’s case specifically, but said in a statement that “we take the integrity of our scientists seriously and we recognize how critical that is to maintaining widespread confidence in our research among the scientific community, policy-makers, and the general public.”

Still, Lundgren is unquestionably accomplished in his field. He's won awards, published dozens of peer-reviewed articles and been widely cited by other scientists. And, according to PEER, he isn’t alone.

PEER has collected allegations by other USDA researchers who haven't yet gone public, but describe pressure not to pursue certain lines of research. The pressure isn’t necessarily as egregious as the kind you find in Lundgren’s account, but there are allegations of verbal discouragement, and a tacit understanding of what sort of research and behavior is unwelcome.

The agency's own guidelines also state that scientists “should refrain from making statements that could be construed as being judgments ... on USDA or any other federal government policy, either intentionally or inadvertently.” That open-ended language—is there any important agricultural research question that doesn't touch on policy?—seems to invite politically motivated interference with science.

“You can do whatever science you like, so long as it doesn't have real-world implications,” says Ruch. “That's a curious stance.” Some attribute these measures to the heavy hand of companies that profit from controversial practices and hold considerable sway within the USDA. Indeed, the USDA has relied on industry-friendly interpretations of science in several recent high-profile actions, including approvals of new genetically modified crops and criticisms of an Environmental Protection Agency neonicotinoid review.

“For the USDA to say that EPA’s analysis was flawed, without any evidence to back that up, was really disconcerting,” says Scott Black, the executive director of the Xerces Society, a conservation group active in neonicotinoid debates. “For USDA to stifle Dr. Lundgren’s objective and quality research, not to mention casting a shadow over legitimate scientific debate, is perhaps even more so.”

Others see a less nefarious USDA desire to avoid bitter controversies between industry and activists, at least in public. Whatever the reasons, it's a disturbing pattern. Nearly half of America's surface is devoted to food production; agriculture affects everyone. And though public debate over pesticides and genetic engineering often descends into hyperbolic posturing, questions about their harms and benefits desperately need to be studied.

It’s hard to make good decisions without good facts. If scientists tiptoe around the most important issues in their field, we'll get neither. That’s why, when President Obama took office, he pledged to restore a scientific integrity corroded during the Bush Administration, when government science was routinely distorted to fit political ends. On our farms, that might still be the case.