The taxpayer-backed bank said it was “extremely sorry” for the problem which affected all four of its banking brands - NatWest, RBS, Ulster Bank and private bank Coutts.
A spokesman said: “We can confirm that the issues customers were experiencing in relation to delayed credits and debits have now been resolved and accounts have been updated. We are extremely sorry for the inconvenience and distress that this has caused our customers.
“If any customers are still experiencing issues please contact our call centres or come into a branch where are our staff are ready to help. We will continue our work to make sure that no customer will be left out of pocket as a result of this issue.”
The bank faced a barrage of customer complaints after it admitted earlier in the week that delayed banking payments may not show up in accounts until the weekend.
The issue also affected some Bacs payments, such as tax credits and disability living allowances.
NatWest and RBS have been hit by a number of embarrassing IT glitches in recent years.
In 2013, RBS’s online service was disrupted by a denial-of-service attack.
Last November, the state-backed group was hit with a £56m fine from the Bank of England and City watchdog Financial Conduct Authority after a computer failure in 2012 saw as many as 6.5 million customers unable to make payments for as long as three weeks.
The outage hit customers at NatWest and Ulster Bank - RBS’s Irish business.
Andrew Tyrie, chairman of the Treasury Select Committee, described the latest RBS problem as a “serious IT failure at RBS, the latest of many in the industry” and said he would write to RBS boss Ross McEwan and regulators for “reassurance that the steps necessary to bring a halt to these failures are being taken”.