Pakn'Save, New World and Four Square customers in the North Island were overcharged for their groceries on Monday after a computer glitch meant a quarter of advertised specials were not registered.
The issue occurred between 7am and 12.30pm across 69 Foodstuffs owned stores.
Foodstuffs' head of corporate affairs, Antoinette Laird, told Newshub about a quarter of the week's new specials were not applied.
"We take getting our prices right, in multiple systems every day, extremely seriously."
She says issues like this are "extremely rare".
"We have systems and processes in place to identify them early. We sincerely apologise to any customers who shopped with us and didn't receive the correct special price they were expecting at checkout."
Laird says any customer who suspects they may be affected should check their receipts and make contact with the store they shopped at to put it right.
It's not the first time an error like this has caused customers to be overcharged.
In 2017 a similar glitch caused issues across Pakn'Save and New World Stores.
A Consumer NZ survey released in April found 46 percent of respondents had been charged more at checkout than the price on the shelf.