NatWest parent Royal Bank of Scotland admitted around 600,000 banking payments that have failed to go through may not apply to accounts until the weekend.
Taxpayer-backed RBS said the issue with its "overnight process" has been identified and fixed, but admitted affected customers of NatWest, Royal Bank of Scotland, Ulster Bank and private bank Coutts may have to wait until Saturday for the payments to show up in their accounts.
A spokesman said: "We have fixed the underlying issue, we apologise for the inconvenience caused and we are working flat-out to get these payments updated for our customers no later than Saturday."
The issue has impacted credits and direct debits and is thought to also include tax credits and disability living allowance payments.
The group was not able to confirm how many customers had been affected, but said the problem did not apply to all accounts.
Twitter lit up with comments about the RBS payments issue, with customers blasting the group over "yet another NatWest blunder" after waking up this morning to find payments missing from their accounts.
The glitch comes just days after the Nationwide building society suffered an IT blackout, with thousands of customers left unable to use its full services for two hours on Monday morning.
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 £56 million fine from the Bank of England and City watchdog Financial Conduct Authority (FCA) 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.
RBS stressed that payments were delayed rather than missing and promised customers they would not be left "out of pocket" by the latest system error.
A spokesman said: "To any customers concerned about the implications of this issue we advise them to come into a branch or get in touch with our call centres where our staff will be ready to help.
"We will ensure no customers are left out of pocket as a result of this issue."
But customers took to Twitter to vent their anger.
Mahbuba Chowdhury (@Mahbuba21) said: "Where is my money #Natwest? I have not been paid this month thanks to you."
Rebecca Rutt (@rebecca_rutt) said: "Why is it that the banks always have technical glitches around payday??" #Natwest
Joy Topping (@joyful2101) said: "Definitely time to find a new bank." #Natwest @NatWest_Help
Imanmade (@imanmade) said: "This is really frustrating! What is going on?? Yet another #Natwest blunder!!" #TimeTochangeBank
El Cid (@1Davidsidney) said: "This lot offered me business advice. I declined." #Natwest
Fatima Saad (@Fksaad82) said: "Finally got through after 40mins apparently there's a problem with natwest and I should contact them!".
Charlie Gwent (@AchtungCharlie) posted a scene from cartoon TV comedy Family Guy where Stewie beats up Brian the dog and repeatedly asks him: "Where's my money, man?"
Guy Anker, managing editor of MoneySavingExpert.com, said: "This is a hugely worrying time for those affected. It's vital anyone with an RBS, NatWest, Ulster or Coutts account that was expecting money today or is expecting money to go out, say to pay a bill, checks their account immediately."
He added: "If you were due to make important payments today such as your mortgage, rent or utility bills, then ensure you let the other person or company know as soon as possible."
The FCA launched a report last March into the amount of time resources boards at financial services firms devote to the resilience of their IT systems after a raft of system errors.
The regulator is expected to issue its updated guidance on IT resilience to financial services firms later this year.
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