A computer glitch saw 12,000 customers of the Co-operative Bank wrongly charged an average of $20 each on Boxing Day.

The bank has refunded and apologised to affected customers, who collectively paid somewhere in the region of $240,000.

The Co-operative Bank chief executive David Cunningham said the error occurred in the small hours of December 26.

"We became aware of the error pretty early on Boxing Day and swung into action so for almost all of those customers the fees were reversed the next day. There were a handful more reversed on December 28 and a small number that were a bit more complicated that have been reversed today."

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Customers who had more than $25,000 of lending or borrowing with the bank were automatically exempt from transaction fees, which were paid by other customers on the 26th of every month.

"The programme that recorded the relationship size didn't run correctly and as a result they weren't recorded as being exempt from fees," Cunningham said.

"We just had two or three people work through methodically what had gone wrong and then corrected it."

The bank had messaged and apologised to the customers via internet banking or email as soon as the error was identified.