The Pepper Group has apologised after 253 customers whose mortgages it services had their monthly repayment deducted twice.
The mistake arose because of an isolated error related to a particular direct debit file.
A spokesman for Pepper said the company is working to rectify the mistake as a matter of urgency.
He added that the company hopes that a majority of the customers will have been fully refunded in the next 24 hours.
"In some cases, however, it may take the receiving bank longer to process the payment into their account," he said.
"We will be writing directly to all the impacted customers to apologise and once all customers have been refunded we'll review the root causes of this issue to prevent a future recurrence."
Pepper said it is still determining why the problem arose and wants to ensure it does not happen again.
Any customers who incur charges as a result of the mistake will have them reimbursed, it said.
Pepper services approximately 60,000 residential mortgages here, many of which were sold to funds by lenders such as Bank of Scotland (Ireland), Permanent TSB, Danske Bank, Ulster Bank and IBRC.