A new system for checking the criminal records of newly-qualified teachers could lead to delays in getting them registered to start work in September, according to the General Teaching Council for Wales.
It fears it could be blamed by schools if teachers are unable to start work on time next term because of the additional paperwork involved.
The Assembly government is bringing forward urgent legislation next week, enabling the GTCW to undertake suitability checks - including Criminal Records Bureau (CRB) checks - on teachers. The aim is for the new regulations to be in place by the end of the month.
Mal Davies, the council's chairman, described the new duty as a knee-jerk political reaction to stories earlier this year exposing registered sex offenders working in English schools.
The GTCW's counterparts in Scotland and England have not been given a comparable responsibility for CRB checks.
The council registers around 1,600 NQTs a year. Carrying out CRB checks means the registration process will take around six weeks, rather than a few days as at present, it says.
At pound;36 for each enhanced check, it will also cost around pound;60,000 a year. The Assembly government has agreed to meet the CRB costs for first-time registrations, but teachers whose GTCW registration has lapsed will have to pay the pound;36 fee if they want to return to the classroom.
A government spokesperson said only a small proportion of teachers - NQTs and lapsed registrations - would be affected by the changes, and noted CRB checks are usually done within four weeks. She added they were being done to safeguard children.
But at last week's GTCW council meeting in Aberystwyth, Mr Davies urged all teachers to complete its registration process as early as possible to avoid any potential backlog which could leave many schools in limbo when the new academic year begins.
The GTCW is also concerned about disruption should experienced teachers allow their council registration to lapse, not realising that, despite remaining in the same post, anyone re-registering after the May 31 deadline will be subject to CRB checks.
Confusion among schools and local education authorities about the GTCW's CRB checks is also likely to lead to increased workload and further delays.
Some employers have already submitted NQTs' details to the CRB as part of the normal job selection process, despite the fact that the GTCW will have to submit the same individual's details at the time of council registration.
Mr Davies said: "The message we need to get out to every new inductee is that they need to register early."
He fears the GTCW could face a backlash if the checking process leads to disruption. He added: "Everyone must understand that the process is going to bodies outside of our control."
Council member Tim Cox said: "I am not convinced that the CRB is going to be able to manage this. It is going to be a nightmare."
But fellow member Ian Guy said the council and teachers had to come to terms with the new legislation for the good of pupils.
"We must not lose sight of the reason why we are embarking on this. There are people out there willing to devote their whole lives to get into contact with children.
"The onus is on us to ensure that these people do not become registered teachers."