A spokesperson for Bank of Ireland has said that all customer accounts that were mistakenly debited twice will be rectified by early tomorrow.
The bank refused to say how many customers were affected by the glitch.
The fault affected some visa debit transactions carried out on the 17 January, which were then debited again last night.
Any customers who incurred fees or inadvertently went overdrawn will be not charged.
But Bank of Ireland said "all other processing was completed as normal".
It also reassured affected customers that they will not be impacted by fees and charges.
Earlier the bank had said in a tweet that it was "aware of a number of debits displaying twice on accounts. Customer's accounts will be adjusted shortly".
It also thanked customers for their patience.