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."
Some customers reported
waiting more up to an hour for an answer from the bank's call centre, on
calls which could be charged at a local rate. The bank said it was
experiencing a "high volume of calls".
HM Revenue and Customs
(HMRC), which oversees some benefits payments, said that some tax
credits and child benefit payments had not gone through, and that those
affected should contact their bank.
Previous problems
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.
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