The extra costs are currently covered by the Better Schools Fund, but the Welsh Assembly government plans to move the money into each authority's annual support grant.
Education officials fear the previously ring-fenced money could be harder to track once it is in the larger pot. Anwen Williams, continuing professional development organiser for Gwynedd, said: "Once it goes into the settlement we have the additional battle to ensure it's used for its actual purpose. We could miss the boat."
Jan Jones, professional development officer for Wrexham, said: "It will be difficult to tell our elected members how much we need each year because there is no way of knowing how many new teachers will need to be catered for."
EPD was introduced last September, to improve teachers' practice and reduce the drop-out rate among newly-qualified staff.
It entitles teachers in their second and third years to an annual allowance of pound;1,000, which can be spent on training of their choice. For many, it has covered the cost of courses and cover for days away from school. The new teachers work closely with heads of department and mentors to achieve development targets.
At Ysgol Rhiwabon secondary, near Wrexham, James Gordon, a 25-year-old science teacher, has used the money to develop his A-level physics and biology knowledge and to achieve several outdoor education qualifications.
"They see the return," he said. "They put value on us and our skills. They just want a completed teacher, able to teach.
"It's down to the schools. A few friends from university didn't get what they should have, but our school makes it a high priority."
A government spokesman confirmed that EPD money will be removed from the Better Schools Fund from next April.
He said: "Alternative funding structures will be established. Preparatory work is still in its early stages, with initial discussions having taken place with education authorities and other partners."
WHY EPD PLAYS ESSENTIAL ROLE
Early professional development helped Paul Gratrix to get to grips with GCSE coursework, understand the transition to A-level and grapple with time management. But it couldn't help him to form a samba band.
Mr Gratrix, a 28-year-old music teacher in his second year, had hoped to use some of his pound;1,000 allowance to buy instruments for the fledgling band, which he believes opens music up to pupils of all abilities.
But Brazilian instruments were not considered essential to Mr Gratrix's professional development. Instead the money has gone on courses and teaching cover at Cwmtawe comprehensive in Swansea. To improve his GCSE marking skills, he attended an AQA exam board course. The grant also paid for teaching cover while he carried out classroom observations at a neighbouring school.
Its sixth form gave him a better understanding of how to prepare 16-year-olds for A-level.
Mr Gratrix said: "The worry is that during your NQT year you're pampered so much that when you finish you'll be thrown in at the deep end and left to struggle. EPD is invaluable."