A spokesperson for the bank urged customers not to resend payments, as they are working on getting them processed again as soon as possible.
However, a later statement made clear the cause of the problem: "As a result of human error, a payment file did not process last night, which means that some transactions applied to some customers accounts since 20 April are temporarily not showing".
"The first some have heard about this is a text message from Ulster Bank telling them they are overdrawn".
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Ulster Bank says "human error" led to money not showing in some customers' accounts.
A spokeswoman said the bank had investigated the issue "as a matter of urgency and have already taken the necessary corrective action which will see recovery actions overnight".
"Card has been declined checked the app and shows my balances not as they should be", another customer said.
Her have reached out to Ulster Bank for more information.
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The Minister for Finance has said the Central Bank is reviewing issues at the bank after some customers claimed money has gone missing from their accounts.
Ulster Bank customers has been blighted by several glitches in recent years and were victim to a major technical fault in 2012 that left them unable to access funds for several weeks. "In some cases, customers may well have missed vital payments as a result of the bank's failure", he said.
Anyone with issues is being asked to contact the bank's customer service team online or on 1850-424-365.
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The bank added that it is "working hard" to fix the issue and apologised for any inconvenience. Now, we are back to a situation where the bank's IT system is failing customers.