The Education Authority (EA) has said it sincerely apologises to substitute teachers who were not paid on Friday as expected.
Some teachers now face a wait until 18 October before they are paid.
The NASUWT union has called on the EA to pay a cash advance.
However, the EA said it had "explored every potential avenue to provide those affected with an interim payment option, but unfortunately no viable option could be identified".
Schools can book substitute teachers through an online system called the Northern Ireland Substitute Teacher Register (NISTR) which is run by the EA.
Substitute teachers can also register their availability on the system.
