The bank is urging customers to not resend payments as they work on the issue
Ulster Bank says "human error" led to money not showing in some customers' accounts.
A number of customers took to social media earlier to highlight issues with transactions that were made since Friday.
Some reported their salaries disappearing from their accounts, with a few they were now in overdraft as a result.
We are aware that some transactions previously applied to accounts for ROI customers since 20/04 are no longer showing. We are working hard to fix this issue and apologise for any inconvenience. https://t.co/25K9Vm8L8H— Ulster Bank Help (@UlsterBank_Help) April 24, 2018
An Ulster Bank spokesperson says: "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 20th April are temporarily not showing.
"We investigated this issue as a matter of urgency and have already taken the necessary corrective action which will see recovery actions overnight.
"We apologise for the inconvenience caused and no customer will be left out of pocket as a result of this issue."
The Finance Minister has said the Central Bank is reviewing the matter, adding that he understands how worrying it can be to find that your money is not in your account.
Paschal Donohoe welcomed the assurance from the bank that no customers will be left out of pocket.
“It is a very concerning development for any customer in any bank in our State to be worried about where their money is gone,” he said.
“It is obviously a matter of concern to me.
“The Central Bank are currently reviewing the matter and I know that Ulster Bank have assured their customers that no customer should be out of pocket due to this issue.”
The bank added that emergency cash is available for impacted customers.
Those affected can contact the bank's customer care team on 1850-424-365, get in touch via webchat or visit their local branch.
The bank notes that not all customers are affected by this.
It also says that there is no connection to the 2012 IT system issue - adding that this was human error.
"The money has not 'disappeared' - this was human error which meant that a payment file did not process as normal", the bank adds.
The result is some transactions are temporarily not showing on accounts - however it says customers money is in the payment file that will be processed "as soon as possible".
Additional reporting: Jack Quann and Michael Staines