Around 600,000 bank account payments went missing after a technical glitch at NatWest owner Royal Bank of Scotland.
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.
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 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.
Guy Anker, the 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."
Twitter lit up with comments about the Royal Bank of Scotland missing payments this morning.
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 the infamous scene from cartoon TV comedy Family Guy where Stewie beats up Brian the dog and repeatedly asks him: "Where's my money, man?"