Businesses are being advised to visit their local Ulster Bank branches if they aren't able to withdraw cash.
It says business customers should take photographic identification and account details or, if they also hold Ulster bank credit cards, use the cash advance service for which the bank said it won't charge a fee.
When it comes to lodgements, those made electronically such as salary, pension or welfare payments which were made after Wednesday, June 20, may not have appeared in accounts.
The bank has assured customers that any lodgements made are accounted for, or receipted, but may be in the backlog of transactions which it's working through at present.
It also said it will stop business customers being charged for missed payments or inadvertently going overdrawn.
"We will ensure that no customer is permanently out of pocket because of this issue," the bank said. "We apologise for the inconvenience caused to our customers and are doing all we can to resolve this issue. If you are out of pocket because of this issue please contact us."
The Payments Council said it is working with the RBS Group, which owns Ulster Bank, to resolve the issue.
"If your situation is complicated it may need to be assessed on a case by case basis, but banks and building societies have pledged to do this as quickly as possible," it said. "You should keep a note of any contact you have made or any documentary evidence showing how you have been impacted."