Abbey, which is now owned by Spanish group Santander, apologised. It said direct debits and standing orders still left customers' accounts with no charges levied. The payments were all processed by 1400GMT, the bank said.
"We apologise to customers for any inconvenience the delay may have caused them. No customers will incur any charges as a result of this problem," an Abbey spokeswoman said.
The bank has not expanded on what caused the problem, but said that it was a technical fault. Abbey has six million current account customers, but only those expecting to have their accounts credited on Wednesday were affected.