 -- Whole Foods isn't the only grocery store that has been accused of overcharging customers with mispriced items.

On Wednesday, New York City's Department of Consumer Affairs announced an ongoing investigation into Whole Foods Market, which has nine locations in the area, saying the chain "routinely overstated" the weight of its pre-packaged products, including meat, dairy and baked goods. But the problem isn't limited to Whole Foods. Aside from the Texas-based chain, the department inspected 119 stores citywide and found a 77 percent violation rate.

Dozens of the other grocery stores in New York City had at least one product type with a mislabeled package, according to city's sweep of 120 stores last fall.

The problem of overcharging customers extends outside New York City. In 2012, Los Angeles Superior Court approved a settlement of $1.1 million paid by Ralphs Grocery Co. on allegations that it overcharged customers at its deli and for other weighed food products plus failing to deduct the weight of packaging. Ralphs did not respond to a request for comment from ABC News.

In states like North Carolina, businesses are allowed a small discrepancy in overcharges. State law in North Carolina allows businesses to have a 2 percent error rate among all the items in the store. This year, five stores have been penalized so far. Last November, nine stores, including Dollar General, CVS, Target and Walgreens were fined in the state for price scanning errors, according to the North Carolina Department of Agriculture and Consumer Services.

"A few years ago, we started fining on the second failed inspection in every occasion and we are seeing stores doing a much better job in keeping their price-scanning systems up to date," a spokesman for the North Carolina department said.

A spokesman for CVS, Mike DeAngelis, said in a statement that the company makes "every effort to ensure that the prices advertised in our stores are accurate."

"Whenever a discrepancy between a posted price and the price being scanned is found, our policy is to honor the lower price," DeAngelis said in a statement to ABC News. "These discrepancies typically occur when a sale sign is not taken down in a timely manner after the advertised sale period is concluded, or there is a delay between an item’s price being changed in our system and the new price being posted at the shelf."

Dollar General, Target and Walgreens did not respond to a request for comment.

Last year, Whole Foods agreed to pay a $800,000 settlement with the City Attorneys of Los Angeles, Santa Monica and San Diego after a statewide investigation uncovered widespread pricing violations in California. Those accusations included failing to deduct the weight of containers for self-serve foods at the salad and hot bars; providing less weight than the amount stated on the label for items sold by the pound; and selling items by the piece instead of by pound, which is required by state law.

Whole Foods denies the allegations of mislabeling weighted products in New York City. Michael Sinatra, a spokesman for Whole Foods, declined to divulge the amount that the Department of Consumer Affairs demanded to settle the dispute. The city said the potential number of violations for all pre-packaged goods in New York City stores is "in the thousands."

“We disagree with the DCA’s overreaching allegations and we are vigorously defending ourselves," Whole Foods said in a statement. "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.”