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New York City's Department of Consumer Affairs (DCA) said Wednesday that an ongoing investigation of Whole Foods Market stores has found systemic overcharging of its customers for prepackaged food.

"The overcharges ranged from [80 cents] for a package of pecan panko to $14.84 for a package of coconut shrimp," the agency said in a statement.

"Our inspectors tell me this is the worst case of mislabeling they have seen in their careers," said DCA Commissioner Julie Menin in a statement.

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In its investigation, the DCA said it tested 80 different package types and found they all had mislabeled weights, adding that 89 percent of the tested packages were not in line with the federal standard for the maximum amount "that an individual package can deviate from the actual weight."

"The overcharges were especially prevalent in packages that had been labeled with exactly the same weight when it would be practically impossible for all of the packages to weigh the same amount. These products included nuts and other snack products (flavored almonds, pecan panko and corn nuts), berries, vegetables, and seafood," it added.

Read More: What the heck to do with Whole Foods

Whole Foods said in a statement: "We disagree with the DCA's overreaching allegations and we are vigorously defending ourselves. We cooperated fully with the DCA from the beginning until we disagreed with their grossly excessive monetary demands. Despite our requests to the DCA, they have not provided evidence to back up their demands nor have they requested any additional information from us, but instead have taken this to the media to coerce us."

Falsely labeling a package carries a first-time fine as high as $950 and up to $1,700 for subsequent violations. "The potential number of violations that Whole Foods faces for all prepackaged goods in the NYC stores is in the thousands," the agency also said.

The investigation was first reported by the New York Daily News.

Shares of Whole Foods were down slightly late morning Wednesday.