Monsanto Co. agreed to pay an $80 million fine to settle federal accusations of accounting violations related to a rebate program for the company's trademark weedkiller Roundup.

The investigation, which Monsanto disclosed in 2011, centers on an incentive program launched in 2009 that aimed to promote Roundup at a time when the product was ceding market share to competitors selling cheaper generic versions of the herbicide.

The SEC said Monsanto didn't properly account for tens of millions of dollars in rebates the company paid to retailers and distributors, the costs of which weren't fully reflected when Monsanto booked Roundup sales, leading Monsanto to "materially" misstate its earnings over a three-year period. The SEC didn't specify the amount by which Monsanto misstated its earnings.

As part of the settlement, three accounting and sales executives at the biotech seed giant agreed to pay a total of $135,000 in penalties to settle individual charges, and Monsanto agreed to retain an independent compliance consultant, the SEC said.

Monsanto agreed to the penalty while not admitting or denying the SEC's allegations, the agency said. The accounting and sales executives also didn't admit or deny the alleged violations.

Monsanto said the company is "pleased to put the matter behind it" and said it was "committed to operating its business with the utmost integrity and transparency and in compliance with all applicable laws and regulations." The settlement didn't require Monsanto to make any further changes to its historical financial statements, after Monsanto already restated results for its 2009 fiscal year through the third quarter of 2011 following an "internal investigation," the company said.

"Financial reporting and disclosure cases continue to be a high priority for the Commission and these charges show that corporations must be truthful in their earnings releases to investors and have sufficient internal accounting controls in place to prevent misleading statements," Mary Jo White, chairman of the SEC, said in a statement.

Though regulators have assessed far larger fines in some other matters, the penalty ranks high among recent SEC accounting fraud cases.

In addition to the settlement, Monsanto Chief Executive Hugh Grant reimbursed the company $3.2 million for cash bonuses and some stock awards received during the period in which the SEC said Monsanto broke the accounting rules, according to the SEC. The SEC's investigation found no personal misconduct by Mr. Grant, and his voluntary return of the bonuses and awards made it unnecessary for the SEC to attempt to force one under U.S. securities rules, the agency said.

Monsanto said in October it set aside $93 million for potential legal and environmental settlements, including one related to the SEC investigation into its accounting for Roundup rebates.

Jean Eaglesham contributed to this article.

Write to Jacob Bunge at jacob.bunge@wsj.com

(END) Dow Jones Newswires

February 09, 2016 15:05 ET (20:05 GMT)