Kraft Heinz to restate earnings for 2016 and 2017, citing employee misconduct
Bottles of Heinz Kraft Co. Heinz brand Tomato Ketchup and Yellow Mustard are arranged for a photograph in Dobbs Ferry, New York, on Wednesday, Feb. 20, 2019.

The SEC investigation launched an internal review, which caused Kraft Heinz to delay filing its annual report twice. Standard & Poor's also put the company on CreditWatch negative.

Kraft Heinz disclosed in February a $15 billion write-down on its Kraft and Oscar Mayer brands, as well as an investigation by the Securities and Exchange Commission into its accounting and procurement practices.

Kraft Heinz said in a filing Monday it will restate its financial statements for 2016 and 2017 by $181 million, after a review into its procurement and accounting procedures discovered employee misconduct.

According to Monday's filing with the SEC, the miscalculations were due in part to recognizing the benefits of costs and rebates in the wrong time period, which the company said it has since corrected.

"During the course of a thorough internal investigation, some discrepancies were uncovered which affected the way earnings were calculated between periods," a Kraft Heinz spokesperson said in a statement to CNBC. "While we don't believe that the misstatements are quantitatively material to any prior period, due to the qualitative nature of the matters identified, the Company determined that it is appropriate to correct the errors in previously issued financial statements."

The spokesman, who said the investigation is "now substantially complete," said the findings did not identify misconduct by members of the senior management team. The company has initiated "employee personnel actions" and "improvements to its internal controls" to address the issues, the filing said. After Monday's filing, Kraft Heinz shares lost 1.4% in premarket trading amid a broad sell-off for the market.

Shortly after the filing was released, Warren Buffett, who has a $10.6 billion stake in Kraft Heinz through Berkshire Hathaway , told CNBC's Becky Quick, "The company has my confidence."

Berkshire Hathaway, Kraft Heinz's largest shareholder, said Saturday it was forced to exclude Kraft Heinz's results from its first-quarter earnings report because it had not yet seen the food company's financials.

Berkshire Hathaway and private equity firm 3G Capital created Kraft Heinz by merging Kraft Foods and H.J. Heinz in 2015. The investment team previously worked together to take Heinz private two years prior.

But the Kraft Heinz deal has created headaches for Buffett. More recently, Buffett has been asked to defend 3G's once-lauded operational excellence, as Kraft Heinz's performance has deteriorated. Shares of the food giant have tumbled more than 24% through the year. The company in February reduced its dividend by 36%.

Berkshire Hathaway in February wrote down over $3 billion related to its investment in Kraft Heinz.

Buffett has since said he overpaid for Kraft. On Saturday, he repeated previously expressed sentiments that both he and 3G under-estimated the strength of retailers like Amazon and Costco . U.S. retailers have reacted to increasing online competition by squeezing brands on margins and turning to private label brands, where the retailers can make higher profit margins. Kraft Foods' portfolio is particularly vulnerable to the shift, with its offering of products like Planters nuts and Maxwell House coffee.

"Time usually works it out but it means capital could have been better deployed in other areas. You can always pay too much for a business. I've done it with stocks many times; I've done it with businesses," Buffett said Monday. "At Berkshire, we have at least a half dozen businesses — and I can't even use a 'we' there — I've got to say I paid too much."

Buffett last year stepped down from the Kraft Heinz board to decrease his travel commitments. Berkshire's Tracy Britt Cool and Gregory Abel still sit on the company's board.

– CNBC's Fred Imbert contributed to this report.