The convenience store specialist, which has 2,800 food shops in the UK, accidentally double charged customers who paid by plastic on Tuesday, July 7.
Sources indicated to The Telegraph that although it is impossible to tell how customers may have been overcharged, the number could run into “the hundreds of thousands.”
It comes amidst a bitter price war in the supermarket sector, as Co-op and its rivals attempt to add sales amid competition from discounters and online rivals.
Some Co-op customers took to Twitter to complain about the problem, suggesting refunds have still not been made.
A spokesman for Co-operative Food admitted: “Due to a processing error customers who shopped with us or used a petrol filling station on 7 July using a credit or debit card were charged twice.
“We would like to apologise to all those affected, and reassure customers that refunds will be made directly in to their accounts within 24 hours.
“We will also reimburse any customers who have incurred bank charges as a result of this error. These customers should contact our customer careline.”
It is the latest blunder for the Co-op, whose problems began in 2013 with the emergence of a £1.5bn black hole at its banking arm.
It later emerged that the Rev. Paul Flowers, the former chairman of its bank, had been caught buying class A drugs, which triggered a major overhaul of the mutual’s corporate governance structure.
The business is now chaired by former Asda boss Allan Leighton, and run by former Wm Morrison finance director Richard Pennycook.
The Co-op sold a number of businesses in order to bolster its balance sheet, and has reduced it stake in the bank to 20pc through a debt-for-equity restructuring and further equity placings.
The food retail business is however one of the Co-operative Group’s strongest divisions, led by chief executive Steve Murrells.
Mr Murrells is aiming to turn Co-op Food in to ‘the number one convenience retailer in the UK,’ by closing down or selling larger stores, refitting existing stores, and opening new branches.
He aims to have 3,000 stores by the end of 2017, and in the last 12 months has completed 500 refits.
