The city's Department of Consumer Affairs said it found mislabelled weights on every single one of 80 different types of prepackaged products. It said the overcharges ranged from 80 cents for a package of pecan panko to $14.84 too much for coconut shrimp.
The watchdog suggested that many Whole Foods packages were never weighed at all. They said in some cases, every package of a product was labelled with exactly the same weight. They say that would be nearly impossible with foods such as vegetables and seafood.
Last year, Whole Foods agreed to pay $800,000 in penalties — and improve pricing accuracy — after an investigation into alleged pricing irregularities in California.
Whole Foods has long battled a reputation for high prices — some derisively call the store "Whole Paycheck" — and it recently announced plans for a new chain of smaller stores with lower prices.
The company has 422 stores in the United States, Canada and the United Kingdom. Whole Foods "never intentionally used deceptive practices to incorrectly charge customers" a spokesman for the Texas-based chain said in a statement, adding the chain will "vigorously defend" itself.