The bank says transactions previously applied to customers accounts since April 20th are no longer showing.
In an update, the bank said it could be tomorrow before the issue is resolved.
Describing it as a "disgraceful situation" Sinn Féin's finance spokesman Pearse Doherty called for the bank to appear before the Oireachtas Finance Committee while it was described as a "cause of serious concern" by Fianna Fail finance spokesman Michael McGrath.
Ulster Bank says "human error" led to money not showing in some customers' accounts.
Various social media users have also said that they have had their Ulster Bank credit and debit cards declined while making purchases.
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Ulster Bank suffered a huge system crash in 2012 that deprived customers of basic banking services for nearly a month.
The statement added that emergency cash of up to €500 is available in branch or over the phone, with the correct identification. No customer will be left out of pocket as a result of this issue.
The bank has said this was as a result of a payment file which did not process last night and has assured customers that the money is still in the payment file and will be processed overnight. "In some cases, customers may well have missed vital payments as a result of the bank's failure", he said. "If you would like to contact us please call our customer care team on 1850 424 365, get in touch via webchat or alternatively visit your local branch".
Human error was behind the disappearance of money, including monthly salaries, from the accounts of Ulster Bank customers over the weekend.
Customers said when they checked the bank's app its shows that their balances are not as they should be.
"We are working hard to fix this issue and apologise for any inconvenience".