NEW teachers due to work their first paid subbing shift today have found their names are missing from a second vital register.
Around 500 newly qualified classroom staff are still waiting to be registered by the General Teaching Council Northern Ireland (GTCNI).
Teachers who want to work in a school must first have a registration number.
The GTCNI said there had been a backlog in processing applications due to problems beyond its control.
It has now emerged that these problems have also affected the Northern Ireland Substitute Teachers Register (NISTR).
Only those on NISTR can be called upon to provide subbing cover in schools.
Many schools had provisionally lined up new teachers for subbing shifts from today.
Young staff have contacted unions fearing that they may not now be able to accept this work due to not appearing on either the GTCNI register or NISTR.
The Education Authority has told unions that it is aware that some have been unable to complete their NISTR registration.
It has written to teachers currently in the process of registration explaining "your TR number is not uploading to the NISTR system as a direct result of the GTCNI system issues".
It said it was working with GTCNI to resolve the problem as quickly as possible - but it may take up to two weeks.
Those with concerns about provisional bookings have been asked to contact the NISTR administration team on Monday morning.
Justin McCamphill, NASUWT National Official for Northern Ireland, said the situation was unacceptable.
"On Friday I was led to believe that the issue was resolved for students who trained in Northern Ireland I was therefore shocked to be contacted by several teachers who had been informed that they could not register as substitute teachers as an IT upgrade at the GTCNI and damaged the NISTR system," he said.
"This is an appalling situation. It is now incumbent on the minister to personally intervene. A guarantee needs to be made to all effected teachers that none of them will suffer any financial detriment.
"Finally, there must be an independent investigation into GTCNI and DE's role in supporting them. GTCNI is funded out of teachers' pockets. They must be accountable to the profession."
The Department of Education has said the situation was "deeply regrettable and the minister has instructed GTCNI to fix this as a matter of urgency and to review the recent changes in their IT systems to ensure that no other unforeseen problems have been introduced".