First Credit Union chief executive Terry Edwards said the issues arose after the migration which took place over the weekend.
"We issued at no direct cost to the member 24,500 new debit cards, these were mailed out progressively over the last month with PIN mailers sent separately," Edwards said.
"Most of the member concerns have been over the change in cards/PINs and we are working really hard with members to sort things out. We are aware that a few merchants aren't accepting our new cards, in some situations, as their own internal setup has not been updated yet. We expect this to be rectified in the next couple of days."
Edwards said the bank did not see issues with the internet banking service, but the method of logging in has changed which has caused confusion for some customers.
"All of our branches and our call centre are really busy and I know members have had difficulty getting through to the call centre, I don't think that has changed and it is our expectation that call centre volumes will remain very high for this week," Edwards said.