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.
"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:
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