About 600,000 payments expected by customers of the RBS group of banks have failed to enter accounts overnight, the bank has admitted.
Payments including tax credits and disability living allowance are among the payments that have failed to be credited to accounts.
RBS admitted that some payments were “missing”, but it had now identified and fixed the underlying problem.
In 2012, the group was hit by a major IT meltdown that led to a large fine.
Customers from RBS, NatWest, Coutts and Ulster Bank – all part of the same group – are thought to have been affected by the issue.
Some 600,000 transactions have been affected and the banking group said it was now trying to update accounts as a “priority”.
“We are aware of an issue with our overnight process which has resulted in some of our customers not having credits or direct debits being applied to their accounts,” a spokesman for RBS said.
“We are working to get this resolved as quickly as possible and apologise to customers for the inconvenience caused.
“To any customers concerned about the implications of this issue, we advise them to get in touch with our call centres or come into a branch where our staff will be ready to help. We will ensure no customers are left out of pocket as a result of this issue.”
The problem only affected a relatively small proportion of payments, the bank said.
However, it is an embarrassment for the group which was fined £56m by regulators after a software issue left millions of customers unable to access accounts.
RBS, NatWest, and Ulster Bank customers were affected in June 2012 after problems with a software upgrade. On that occasion, the IT failure affected more than 6.5 million customers in the UK over several weeks.
The banking group said it had invested hundreds of millions of pounds to improve its computer systems since then.