Mushrooms priced at $4.99 were twice $2 more at the checkout, avocados advertised at three for $5 were charged at $1.99 each and sliced salmon going for $8.99 on the shelf cost $10.79 at the checkout four times.
Pak'nSave Māngere owner Michael Kennedy says he accepts the findings.
"It is disappointing for me that these issues occurred, as I take pricing and getting it right extremely seriously," he told the Herald.
"As soon as I was aware, significant steps were taken to minimise the chance of this happening again, including additional training in-store.
"We try not to make mistakes, but if we do, we always work to correct them."
Commerce Commission officials carried out "mystery shops" to check advertising prices against those charged at checkout.
The mystery shoppers told customer service staff at Pak'nSave about the price differences, but when they returned the next day and bought the same items, shoppers were still being charged more at the till than what was displayed on shelves.
Kennedy says his Pak'nSave team understands the significance of keeping a watchful eye on ticketing and price verification.
Foodstuffs, the company which owns the Pak'nSave brand, head of corporate affairs Antoinette Laird says the trust of customers is of the utmost importance.
"Our stores take pricing and getting it right seriously," she says.
"If a customer ever feels they've been charged an incorrect amount, they should notify a staff member so we can look into it and correct it immediately if an issue has occurred."