The group said an issue with its “overnight process” meant some customers of NatWest, Royal Bank of Scotland, Ulster Bank and private bank Coutts had not seen credits or direct debits applied to their accounts.
An RBS spokesman said the issue had been identified and fixed, but it was still working to retrieve missing payments.
He 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.”
NatWest’s Help Twitter account has been bombarded with tweets from worried customers who have woken up this morning to find payments missing from their accounts.
The group was not able to confirm how many customers had been affected, but said it was not all accounts.