The trouble started, the S.E.C. said, when the economy was in a tailspin and Monsanto’s customers were flocking to less expensive generic versions of Roundup. Recognizing that sales of the product were coming in well below what the company had forecast to investors, Monsanto decided to change its accounting policies on customer rebates, the whistle-blower said. Monsanto essentially shifted the costs of the rebates into fiscal 2010 while keeping the sales associated with the rebates in 2009.

Although the S.E.C. did not accuse the Monsanto employees of intending to violate the law, it said in its settlement order that “as a result of the improper accounting, Monsanto met consensus earnings-per-share analyst estimates for fiscal year 2009.” Meeting such estimates is crucial: When companies report results that are below expectations, their stocks often plummet.

In 2010, the company again shifted some rebate costs into the next year. The actions inflated Monsanto’s reported profit by $31 million over the two years, according to regulatory filings.

In late 2011, after the S.E.C.’s investigation began, Monsanto said it would restate its earnings to reflect the proper timing of revenue and costs related to the rebates. Although the impact amounted to only a few pennies a share during the period, in its February settlement with the S.E.C., Monsanto paid $80 million in penalties. The company neither admitted nor denied the accusations but agreed to hire a qualified independent ethics and compliance consultant.

In the enforcement action, the S.E.C. named three midlevel employees involved in the improper activities. They paid a total of $135,000 in penalties. One had retired from Monsanto, the S.E.C. said, but the other two still work at the company. Both are accountants and were barred from appearing before the S.E.C. as accountants for one to two years.

It was frustrating, the whistle-blower said, that the S.E.C. took no action against others at Monsanto who, he said, knew about the improprieties.

“It’s really difficult when your company is doing something you know is wrong but you’ve got everybody around you saying it’s perfectly fine,” the former employee recalled. “The Monsanto culture is very tightknit. Everybody has stock options and everyone is financially at risk. So they go with the flow.”