Kraft Heinz will pay $62 million to settle accusations of an accounting ‘scheme.’

When Kraft merged with Heinz in 2015, it was meant to be another chance for the private equity firm 3G Capital to apply the same ruthless cost savings it had already introduced at Heinz and had used throughout the consumer goods industry. But at Kraft Heinz, the strategy was pushed too far, federal regulators said.

On Friday, the Securities and Exchange Commission said it had charged the packaged food giant and two former executives with a “scheme” to inflate those cost savings. Kraft Heinz will pay $62 million to settle the case.

“Kraft and its former executives are charged with engaging in improper expense management practices that spanned many years and involved numerous misleading transactions, millions in bogus cost savings and a pervasive breakdown in accounting controls,” Anita Bandy, an associate director of the S.E.C.’s enforcement division, said in a statement.

“Kraft and its former executives are being held accountable for placing the pursuit of cost savings above compliance with the law,” she added.

Kraft Heinz has “fully cooperated” with the S.E.C. investigation, said Kathy Krenger, a spokeswoman for the company.

“The internal control weaknesses we identified and disclosed in 2019 were fully remediated in 2020,” Ms. Krenger said. “Kraft Heinz is much stronger today because of the actions we took and embedded into our company culture.”

The company neither admitted nor denied the S.E.C.’s findings.

Kraft Heinz set performance targets for its procurement division tied to achieving cost savings that the company had promised investors in the wake of the merger, the S.E.C. said in its lawsuit. But by 2017, Kraft Heinz had “largely exhausted its ability” to extract more savings from the 2015 merger, just as it as was facing inflationary headwinds.

Kraft Heinz’s former chief operating officer Eduardo Pelleissone continued to push for “unreasonable” levels of cost savings, the suit alleges, and the division improperly recognized 59 transactions.

The suit charges Mr. Pelleissone with ignoring warning signs of the accounting misconduct and the company’s former chief procurement officer Klaus Hofmann with failing to design effective accounting controls.

Mr. Pelleissone agreed to penalties totaling $314,211. Mr. Hofmann agreed to a fine of $100,000 and a ban on serving as an officer or director of a public company for five years.

Lawyers for Mr. Pelleissone and Mr. Hofmann did not immediately respond to requests for comment. Neither man admitted wrongdoing.

Kraft Heinz first disclosed the S.E.C. inquiry in early 2019, the same day it announced it would be writing down the value of its Kraft and Oscar Mayer brands by more than $15 billion, sending its shares in a tailspin. As the company worked through issues with regulators, it twice delayed its annual report and unveiled further write-downs of its well-known brands.

Warren E. Buffett, whose Berkshire Hathaway teamed up with 3G on the 2015 merger, has since said he “overpaid” for the packaged food giant. Berkshire owns a little over a quarter of the company.

A number of senior executives have left Kraft Heinz since the 2019 disclosure, including Bernardo Hees, who had served as chief executive, and David Knopf, who had been the chief financial officer.