The reputation of Roundup, whose active ingredient is the world’s most widely used weed killer, took a hit on Tuesday when a federal court unsealed documents raising questions about its safety and the research practices of its manufacturer, the chemical giant Monsanto.

Roundup and similar products are used around the world on everything from row crops to home gardens. It is Monsanto’s flagship product, and industry-funded research has long found it to be relatively safe. A case in federal court in San Francisco has challenged that conclusion, building on the findings of an international panel that claimed Roundup’s main ingredient might cause cancer.

The court documents included Monsanto’s internal emails and email traffic between the company and federal regulators. The records suggested that Monsanto had ghostwritten research that was later attributed to academics and indicated that a senior official at the Environmental Protection Agency had worked to quash a review of Roundup’s main ingredient, glyphosate, that was to have been conducted by the United States Department of Health and Human Services.

The documents also revealed that there was some disagreement within the E.P.A. over its own safety assessment.

The files were unsealed by Judge Vince Chhabria, who is presiding over litigation brought by people who claim to have developed non-Hodgkin’s lymphoma as a result of exposure to glyphosate. The litigation was touched off by a determination made nearly two years ago by the International Agency for Research on Cancer, a branch of the World Health Organization, that glyphosate was a probable carcinogen, citing research linking it to non-Hodgkin’s lymphoma.

Court records show that Monsanto was tipped off to the determination by a deputy division director at the E.P.A., Jess Rowland, months beforehand. That led the company to prepare a public relations assault on the finding well in advance of its publication. Monsanto executives, in their internal email traffic, also said Mr. Rowland had promised to beat back an effort by the Department of Health and Human Services to conduct its own review.

Dan Jenkins, a Monsanto executive, said in an email in 2015 that Mr. Rowland, referring to the other agency’s potential review, had told him, “If I can kill this, I should get a medal.” The review never took place. In another email, Mr. Jenkins noted to a colleague that Mr. Rowland was planning to retire and said he “could be useful as we move forward with ongoing glyphosate defense.”

The safety of glyphosate is not settled science. A number of agencies, including the European Food Safety Agency and the E.P.A., have disagreed with the international cancer agency, playing down concerns of a cancer risk, and Monsanto has vigorously defended glyphosate.

But the court records also reveal a level of debate within the E.P.A. The agency’s Office of Research and Development raised some concern about the robustness of an assessment carried out by the agency’s Office of Pesticide Programs, where Mr. Rowland was a senior official at the time, and recommended in December 2015 that it take steps to “strengthen” its “human health assessment.”

In a statement, Monsanto said, “Glyphosate is not a carcinogen.”

It added: “The allegation that glyphosate can cause cancer in humans is inconsistent with decades of comprehensive safety reviews by the leading regulatory authorities around the world. The plaintiffs have submitted isolated documents that are taken out of context.”

The E.P.A. had no immediate comment, and Mr. Rowland could not be reached immediately.

Monsanto also rebutted suggestions that the disclosures highlighted concerns that the academic research it underwrites is compromised. Monsanto frequently cites such research to back up its safety claims on Roundup and pesticides.

In one email unsealed Tuesday, William F. Heydens, a Monsanto executive, told other company officials that they could ghostwrite research on glyphosate by hiring academics to put their names on papers that were actually written by Monsanto. “We would be keeping the cost down by us doing the writing and they would just edit & sign their names so to speak,” Mr. Heydens wrote, citing a previous instance in which he said the company had done this.

Asked about the exchange, Monsanto said in a second statement that its “scientists did not ghostwrite the paper” that was referred to or previous work, adding that a paper that eventually appeared “underwent the journal’s rigorous peer review process before it was published.”

David Kirkland, one of the scientists mentioned in the email, said in an interview, “I would not publish a document that had been written by someone else.” He added, “We had no interaction with Monsanto at all during the process of reviewing the data and writing the papers.”

The disclosures are the latest to raise concerns about the integrity of academic research financed by agrochemical companies. Last year, a review by The New York Times showed how the industry can manipulate academic research or misstate findings. Declarations of interest included in a Monsanto-financed paper on glyphosate that appeared in the journal Critical Reviews in Toxicology said panel members were recruited by a consulting firm. Email traffic made public shows that Monsanto officials discussed and debated scientists who should be considered, and shaped the project.

“I think it’s important that people hold Monsanto accountable when they say one thing and it’s completely contradicted by very frank internal documents,” said Timothy Litzenburg of the Miller Firm, one of the law firms handling the litigation.

The issue of glyphosate’s safety is not a trivial one for Americans. Over the last two decades, Monsanto has genetically re-engineered corn, soybeans and cotton so it is much easier to spray them with the weed killer, and some 220 million pounds of glyphosate were used in 2015 in the United States.

“People should know that there are superb scientists in the world who would disagree with Monsanto and some of the regulatory agencies’ evaluations, and even E.P.A. has disagreement within the agency,” said Robin Greenwald, a lawyer at Weitz & Luxenberg, which is also involved in the litigation. “Even in the E.U., there’s been a lot of disagreement among the countries. It’s not so simple as Monsanto makes it out to be.”