Unlike the English system, funds to reward teachers who cross the new pay threshold in Wales will be distributed via local authorities - who can keep any money left over. Councils have already been given the money, on the basis that three-quarters of teachers at the top of the current pay scale will get the increase.
Nigel de Gruchy, general secretary of the National Association of Schoolmasters Union of Women Teachers, said: "There is potential for money to be creamed off and an incentive for heads not to pass it on to teachers if it means the money can be saved and spent in other ways."
Similar fears about the Government's pound;50 million boost for Welsh schools - part of Gordon Brown's Budget last week - have been allayed by the assembly.
Heads had voiced concern at last weekend's annual conference of the National Association of Head Teachers in Cardiff. But the assembly this week said that pound;20.3m earmarked for schools would go straight into their budgets - as in England.
Another pound;25m will go on capital invstment in schools, while pound;4m is being held back for future projects. Finance secretary Edwina Hart said the money should be used to "raise standards of teaching and learning - including repairs and maintenance".
Rosemary Butler, assembly education secretary, ended speculation over responsibility for the new pay structure in her address to the NAHT conference. As a pay and conditions matter, it fell under the Department for Education and Employment in London, she said, not the assembly.
Headteachers in Wales are paid less than heads anywhere in England, David Hart, the association's general secretary, told the conference. Eighty per cent of heads in Wales were on the bottom six points of the pay spine, compared with only 40 per cent in Merseyside, 50 per cent in the East Midlands and 20 per cent in London.
Anne Hovey, NAHT regional officer for Wales, said the union's research revealed that the discretion available to governing bodies to pay more than the minimum had rarely been used.
Some authorities exposed heads to "moral blackmail", warning that if they paid themselves more, someone else faced redundancy, said Alun Jones, director of NAHT Cymru.