Thousands of customers of the Yorkshire and Clydesdale banks face having to pay more for their mortgages after a "rounding error" was made when a system was upgraded.
The miscalculation has affected 18,000 variable mortgage rate customers, who now face increases in their mortgage payments.
A spokesman at Yorkshire Bank said in 2005 changes were made to a system to introduce extra facilities such as mortgage holidays and overpayments, and the error was made.
"We applied some changes to our mortgage systems to add more features for customers. Unfortunately, this created an error in the way that some regular mortgage payments were calculated.
"This calculation error, when combined with last year's unprecedented rapid reduction in interest rates, resulted in some customers' regular payments falling below the minimum required to complete the mortgage within the agreed term," said a bank statement.
Based on the calculation in 2005 the system would adjust payments when interest rates changed.
The spokesman said the changes were made in 2005 but did not appear as a problem until the credit crunch aftermath, when interest rates were continuously cut.
The banks said they were sorry and are working with customers "to remedy the situation in the most appropriate way for their individual circumstances".