The commission said the promotional pricing was advertised online on Pak'NSave website and on price tags and signs in stores.
The charges arose from finding the price discrepancies were still occurring. The matter is now before the courts.
Foodstuffs, which operates the Pak'nSave supermarket chain, along with New World and Four Square chains, has been contacted for comment.
Each Pak'nSave supermarket is individually owned, Foodstuffs licences the operation of supermarkets through a franchise arrangement.
Michael Kennedy, owner-operator of Pak'nSave Mangere, acknowledged the charges over "pricing issues" at his store.
"We take pricing and getting it right extremely seriously. As soon as we were aware, immediate steps were taken to minimise the chance of this happening again, including additional training in-store," Kennedy said.
"We try not to make mistakes, but if we do, we always work to correct them."
The commission was unable to comment further on the matter.
The Herald understands Mangere Pak'nSave is not the only store in the supermarket chain to have price discrepancies in the past. One consumer told the Herald price discrepancies between prices advertised and those charged at the till had also occurred at a store in Thames.
A spokeswoman for Foodstuffs North Island said the company took the accuracy of its pricing in its franchised stores "very seriously".
She said the business had a "variety of systems in place" to ensure prices accurately reflected prices advertised and shown on supermarket shelves, including "internal training processes, compliance manuals and price integrity managers who assist with the process".
"Owners, and staff, are reminded regularly of the need for accuracy," she said.
"While we understand ticketing issues can occur and are usually a result of human error, this case is a reminder of how important it is to ensure accuracy between the shelf price and the till price, particularly with items on promotion. Owners and their teams know how important it is we get it right."
Jessica Wilson, head of research at Consumer, said retailers who misled consumers over the price of goods risked breaching the Fair Trading Act, and could face a fine of up to $600,000.
"The Act gives stores some leeway if [retailers] make a genuine pricing mistake. However, a retailer would have a hard time justifying multiple incorrect prices as 'genuine' errors," Wilson said.
"If you've been charged more at the checkout than the price displayed on the shelf, ask the store why the price is different. Ask it to honour the advertised price.
"If you think the store is misleading you, make a complaint to the Commerce Commission."
There are 45 Pak'nSave supermarkets located throughout the North Island.
