In the letter, issued Tuesday, the Food and Drug Administration addressed John Mackey, who co-founded and has overseen the company since 1978. Whole Foods was acquired by Amazon in 2017 for just over $13 billion.
The FDA, which reviewed the history of food recalls for the company, claimed that it "engaged in a pattern of receiving and offering for sale misbranded food products."
From October 2019 to November 2020, the FDA said, the company had recalled 32 food products due to undeclared allergens. The agency cited similar recall patterns in previous years.
Grocery products are required to declare all major food allergens under the federal Food, Drug and Cosmetic Act, the agency said, detailing five of 32 recalls in the year through November 2020.
In order to prevent their recurrence or other violations, Whole Foods is "responsible" for investigating and determining the causes of each one, the agency said.
The company is also required to take "prompt action" to correct the violations if it hasn't already, the FDA said. Failure to do so may lead to further enforcement, including seizures or injunctions, the agency warned.
A Whole Foods Market spokesperson told FOX Business that the company takes food safety very seriously and is working "closely with the FDA to ensure all practices and procedures" in its stores "meet if not exceed food safety requirements."
The chain has 15 working days to respond to the FDA letter.