At least two councils are to stop paying for training for aspiring headteachers and others are cutting back on numbers because of budget pressures.
The difficulties come as the national professional qualification for headship (NPQH) is due to become a requirement for first-time heads in Wales from next September.
Councils say the problem is that funding for NPQH training comes out of the same section of the budget as that for inducting newly-qualified teachers and providing professional development for teachers in their second year.
Induction is a statutory requirement but funding is on a formula basis, rather than according to the number of NQTs. So if schools recruit more NQTs than expected, less cash is left for NPQH.
It is ironic that the problem has arisen this year as hundreds of newly-qualified teachers are still looking for jobs.
The Welsh Assembly government says only a limited number of authorities have been affected. Councils can move money from other budgets to fund NPQH if they want. And a spokeswoman said it was looking at ways of making funding more responsive to the distribution of NQTs between LEAs and across Wales.
The National Union of Teachers Cymru is calling for a delay in making NPQH compulsory until the funding issue is resolved, while some education authorities want the cash distributed centrally - either by the Assembly government or the General Teaching Council for Wales (GTCW) - according to demand.
No NPQH candidates will be funded in Denbighshire in 2005-6 because of an anticipated shortfall of pound;102,000. Sylvia Jones, senior education officer, said it had expected around 20 NQTs in the current year but schools registered 56.
It is estimating that induction and early professional development will cost pound;285,000 next year, when it has only been allocated pound;183,000 to cover these activities - plus NPQH and other professional development, for example, for middle managers.
She wants the funding taken out of the "better schools fund" and allocated centrally by the Assembly government or the GTCW.
She said: "Without being able to fund NPQH, we are disadvantaging future heads. Some candidates say they will fund themselves to move on in their careers."
In Wrexham, Merfyn Lloyd Jones, the chief education officer, has written to eligible NPQH candidates suggesting they find alternative sources of funding, such as career development bank loans or their school.
Gethin Lewis, secretary of NUT Cymru, said the problems showed that not enough cash had been allocated for NQT induction, despite it being a statutory requirement.
"Senior teachers, experienced teachers, are going to be discriminated against," he said. "Those who can afford it will do the training. Those who can't, won't."
The union is writing to Jane Davidson, education and lifelong learning minister, calling for a delay in making NPQH compulsory in Wales.
Brian Rowlands, secretary of the Secondary Heads' Association Cymru, said it had concerns not only about funding but how candidates were selected for NPQH. He supported calls for the GTCW to handle the cash for NQT induction and NPQH.
He added: "We are concerned that not enough secondary teachers are going through NPQH, given the age profile of heads (more than 60 per cent are due to retire in the next 10 years)."
Anna Brychan, director of the National Association of Head Teachers Cymru, said the problems were another example of the "fog" surrounding education funding in Wales. "NPQH must be funded on a needs basis. or we will not have enough properly qualified professionals to take up headships as the present cohort retires."