Backlash over Whole Foods pricing investigation

A person bikes past a Whole Foods Market in Brooklyn, New York.
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A person bikes past a Whole Foods Market in Brooklyn, New York.

Shoppers were up in arms regarding accusations that Whole Foods Market has been overcharging consumers for its prepackaged food, including several who threatened to boycott its stores.

The accusations were brought by New York City's Department of Consumer Affairs, which said on Wednesday that after testing 80 various package types from the high-end grocer, all had mislabeled weights.

"Shame on you, Whole Foods! I was aware that your prices were ridiculously high but to lie to your customers & blatantly rip them off, shame shame," Julie des Tombe wrote on the company's Facebook page.

Read MoreWhole Foods overcharging for prepackaged goods: NYC

"Your overcharging practices are deplorable!" Denise Kolby Federoff wrote. "I no longer shop at Whole Foods. Far better, more honest, less expensive choices out there!"

Whole Foods, which said in a statement earlier this week that it disagrees with the DCA's "overreaching allegations," and that it has been cooperating fully since the investigation began, also issued a statement on Facebook:

As always, we appreciate the lively dialogue and feedback of our customers. That said, we ask that you are always...

Posted by Whole Foods Market on Thursday, June 25, 2015

A few consumers defended the high-end grocer, which has a reputation for selling pricier foods. The company recently announced plans for a new value-focused brand, called 365 by Whole Foods Market, which will launch in 2016.

Whole Foods shares were trading slightly lower on Friday.

—CNBC's Fred Imbert contributed to this report