Whole Foods
An organically grown Heirloom tomato is seen in the produce section at the Whole Foods grocery story in Ann Arbor, Michigan, March 8, 2012. Reuters/Rebecca Cook

Whole Foods Market Inc. (NASDAQ:WFM) will pay about $800,000 in penalties and fees for overcharging customers in California.

State and local inspectors found that the natural and organic foods retailer didn’t subtract the weight of the containers when weighing food and sold some prepared foods by item rather than weight, the Associated Press reported Tuesday.

Prosecutors said that the pricing discrepancies violated consumer protection laws regarding false advertising and unfair competition.

Whole Foods must pay $210,000 to each of the city attorneys of Santa Monica, Los Angeles and San Diego who originally brought the case. The Austin, Texas company must also reimburse county and state agencies for the cost of the investigation and pay $100,000 to a weights and measures enforcement fund.

Under the agreement covering five years, all of Whole Foods 74 California stores will also be subject to random quarterly audits.

Whole Foods said in a statement that prices were accurate 98 percent of the time and that it cooperated with the investigation.

The company, which had sales of $12.9 billion last year, operates more than 380 stores throughout the United States, Canada and the United Kingdom.