Customer service agents and the bank's helpdesk were hit with a barrage of complaints for the second time in a week after another embarrassing technical failure.
"We are currently missing a batch of credits however we are investigating this as urgent," advisers told customers online.
On its Twitter helpdesk service the bank apologised to customers and said they were working to have the issues fixed as soon as possible.
There was no immediate comment from the bank in Northern Ireland or the Republic.
On its Twitter account, the bank said: "Some customers are experiencing issues this morning. We are working hard to get this fixed...it should be back up and running again very soon...Our online banking is very safe and secure to use, although we would advise caution."
Many customers claimed they were unable to access current transactions, wages being paid into accounts and other payments.
Ulster Bank's parent company Royal Bank of Scotland suffered a major IT fault last week that left customers unable to use debit or credit cards for a three-hour spell on what was expected to be the busiest online shopping day before Christmas.
An estimated 750,000 RBS, NatWest and Ulster Bank customers were affected.
Days later, its websites fell victim to a cyber attack which also affected some customers.
RBS, 80% owned by the UK Government, has been beset by system failures, including a major meltdown last summer, and RBS chief Ross McEwan admitted it had not invested properly for decades.
Ulster Bank revealed that some of its customers with euro accounts were affected in the latest issue.
It is understood the problem centres on payments coming into accounts held in the Republic and payments being made in euros.
"Some inward credit transfer files were delayed through our payment system overnight and we are working to resolve this issue for customers as soon as possible," the bank said in a brief statement.
It is not known how many customers or payments have been affected by the glitch.