Bank of Ireland has confirmed it is experiencing technical difficulties which have resulted in funds not going through to a number of bank accounts.
Teachers, gardaí and civil servants at the Department of Justice and Department of Education have not received their payments as a result.
Pension payments have also been affected.
Bank of Ireland has apologised for the issues and said it is working to resolve the issue.
However, it will not confirm the number of accounts affected by the error.
The bank says all salary and pension payments will be in customers' accounts by tomorrow morning.
AIB said it has been advised that there is an issue with incoming credit transfers from Bank of Ireland.
We can confirm a payment file was delayed last night and payment will credit tomorrow morning. Sincere apologies for this.— Bank of Ireland (@talktoBOI) July 31, 2014
In a statement, Bank of Ireland said the delay only affected one file and the majority of payments will be processed "in a timely manner".
It said that customers will not face charges for unpaid direct debits as a result of delayed payments.
The Irish National Teachers' Organisation said the delay in paying salaries to primary teachers had caused a great deal of worry, disruption and unnecessary hardship.
General Secretary of the Public Service Executive Union Tom Geraghty said more than 100,000 people have been affected by the payment delay.