Ulster Bank says a limited number of customers are experiencing a slight delay in the processing of payments. The bank says the issue is related to the Single Euro Payments Area scheme and not the IT problem at ATMs in the North.
Ulster Bank says any affected customers will have their payments processed overnight.
Meanwhile the bank is to refund customers in the North after double-charging them for withdrawals over a 24-hour period on Monday and Tuesday.
The bank said it is not clear how many customers are involved or how much money was inadvertently withdrawn.
Those affected made withdrawals between 4:15pm on Easter Monday and 4:15pm on Tuesday.
Ulster Bank has apologised to customers and says they will not be left out of pocket as a result.
The bank has been hit by a range of computer problems over the last two years - a number of which have been linked with its parent company, RBS.