Whole Foods Chief Executive John Mackey and his Co-CEO Walter Robb on Wednesday said they were sorry for overcharging customers at the retailer's New York City stores, The Associated Press reported.

The apology comes just days after New York's Department of Consumer Affairs accused the grocery chain of routinely overstating the weight of prepackaged meat, dairy and baked goods at its outlets in the nation's largest city. Commissioner Julie Menin called the practice "incredibly troubling" and noted that Whole Foods continued to overcharge customers even after her agency had brought the issue to the retailer's attention.

"Straight up, we made some mistakes," Robb admitted in a video message. "We want to own that and tell you what we're doing about it."

Robb and Mackey, who in the past has advocated for what he calls "conscious capitalism," insisted the overcharges were unintentional and that they primarily occurred with packaged fresh foods, such as sandwiches and juices, the Business Insider detailed.

To fix the problem, Whole Foods will now retrain employees in New York stores and across the United States, implement a third-party auditing system and refund customers for the full price of any product that has labeling errors.

"It's understandable sometimes that mistakes are made; they are inadvertent. They do happen because (ours is) a hands-on approach to bringing you fresh food," Robb explained.

But Mackey said that the company now strives to be "perfect in this area."

"We don't want there to ever be any mistakes," he added.

The co-CEO insisted that only "a very, very small percentage" of prepackaged food was affected by the overpricing, but New York City inspectors have reportedly found more than 800 violations at the chain's New York stores since 2010, the Consumerist recalled. Customers were charged an extra between 80 cents and $15.

Mackey, for his part, encouraged Whole Foods customers to ask cashiers to check on any suspected error in pricing.

"And if there's a mistake that's not in your favor, we promise to give you that item for free," he said.