They believe Welsh-speaking teachers will be lured away to the increasing number of non-school jobs which require Welsh.
Pay and conditions are not devolved to the Welsh Assembly and schools follow scales agreed in Westminster to ensure equality on both sides of the border.
But Heledd Hayes, Welsh education officer of the National Union of Teachers, believes the new national pay scales are likely to have a particularly detrimental effect on Welsh-medium schools.
Since devolution in 1999, many Welsh-speaking jobs have been created in the Welsh Assembly and Welsh media.
This has attracted a large number of Welsh-speaking graduates away from teaching.
Dr Hayes said: "People who want to use Welsh in their working lives used to see teaching as an attractive option. There's no doubt the new pay scales make it less so."
Iwan Guy, of the National Association of Head Teachers, agreed. He said:
"This is not going to encourage new graduates into teaching."
But he will not be calling for the devolution of pay and conditions. Welsh schools, he believes, suffer under the Assembly's system of funding, which channels all funds through local authorities.
"Devolving pay is likely to work to Wales's disadvantage," he said.
"Teachers in Wales are generally happier than in England, except over funding.
"With anything regarding money, we're far worse off."