Standard & Poor's on Monday placed Kraft Heinz on CreditWatch negative after the struggling food giant failed to file its annual report with the Securities and Exchange Commission even after an extended deadline.

Kraft Heinz shares, which are valued at nearly $39 billion, fell more than 1 percent on the news, at one point sinking to a 52-week low of $31.53.

Last month, the company wrote down $15.4 billion on its namesake Kraft and Oscar Mayer brands, slashed its dividend and disclosed a subpoena from the SEC. Since that announcement, shares of Kraft Heinz have dropped more than 33 percent.

Executives told investors when they were delivering the bad news in February that the company is planning to use divestitures to pay down its debt. CNBC has previously reported that it is weighing sales of its Maxwell House coffee brand and its dairy business.

The following week, it announced that it would not be able to meet the SEC deadline to file its annual report for fiscal 2018. The commission granted Kraft Heinz a 15-day extension to file the report, but the company missed the extended deadline Thursday.

"We are working toward filing our 10-K in the coming weeks once we complete our internal reviews of our accounting practices and procedures related to the procurement area," Kraft Heinz spokesman Michael Mullen said in a statement.

The rating agency could lower or affirm its ratings for Kraft Heinz, including its BBB long-term issuer credit rating and A-2 short-term issuer credit rating, after it concludes a review. S&P said it plans to resolve the CreditWatch after analyzing the annual report once it is filed, in addition to its filing for the first quarter of fiscal 2019.