They also pledged items found to be overpriced will be offered free.
Standing in front of the fruit section of a New York Whole Foods, they said the mistakes were unintentional and the company will increase training to prevent pricing errors from happening again.
"Straight up, we made some mistakes," said Robb. "We want to own that and tell you what we're doing about it."
They made no offer of compensation for errors made thus far, though the New York Department of Consumer Affairs said it found mislabelled weights on every single one of 80 different types of prepackaged products it tested in eight New York stores.
It said the overcharges ranged from 80 cents for a package of pecan panko to $14.84 too much for coconut shrimp.
Robb agreed there were errors, but said some were in the customers' favour, while others charged too much.
"Any claim that we are systematically overcharging customers is completely inaccurate," the company said in a statement.
Mackey said the errors involved fresh food such as juices, cut fruit and sandwiches, packaged in the stores, rather than a central facility. He said they were a result of both human error and poorly calibrated scales.
He also pledged money back from now on if customers discover produce that is mislabelled.
"We want to give 100 per cent guarantee to our customers," Mackey said. "If for any reason you think there's a mistake with any of our products, ask the cashier to check on it, and if there's a mistake that's not in your favour, we promise to give you that item for free."
Last year, Whole Foods, known for its high prices, agreed to pay $800,000 in penalties — and improve pricing accuracy — after an investigation into alleged pricing irregularities in California.
With this pricing scandal, the company is pledging an internal auditing process and a report to customers in 45 days on its progress.
In a statement, Commissioner Julie Menin said that the Department of Consumer Affairs was "gratified" that Whole Foods admitted to issues with its prepackaged food labels.
Based in Austin, Texas, Whole Foods Market Inc. operates 422 stores around the world.