Most schools have increased their salary bills on senior staff during an exercise that was supposed to free cash to pay for their progression up the salary scale.
All headteachers have had to restructure their staff to take into account teaching and learning responsibility payments (TLRs) for senior teachers.
Some staff who will lose allowances under the new criteria could now miss out on salary increases of pound;1,200 because heads have overspent their pay bill.
A TES survey shows salary bills in almost nine out of 10 secondary schools will increase as a result of TLRs, despite schools cutting the number of promoted posts.
Heads reported their schools would be up to pound;100,000 a year worse off as a result of the changes which will cost some teachers up to pound;10,500 a year.
Savings from the introduction of TLRs were supposed to pay for "the substantial majority" of teachers to move to UPS3, the top point on the upper pay scale.
But pay cuts for some teachers have been offset by increases for others and by the cost of growing numbers of support staff employed to free teachers from administrative tasks, heads said.
So this means that fewer teachers will progress to the top of the upper pay scale.
The survey was seized upon by opponents of the changes who said it had "cut a scythe through teachers' salaries".
But claims by the National Union of Teachers which said that the replacement of management allowances with TLRs would call time on teachers'
pastoral role are premature, the survey suggests. Two out of five schools said they would increase the number of pastoral posts filled by staff who are not qualified teachers, but the majority of schools will continue to employ teachers as heads of year.
Lawrence Montagu, head of St Peter's high school in Gloucester, said: "I do not have a problem relating allowances to teaching and learning but I would not take pastoral work away from teaching staff. The two are interwoven."
Fifty-eight schools responded to the survey which was sent to a representative sample of 200 secondaries.
All schools were expected to complete a review of staffing setting out which posts would attract TLRs by the end of December. Teachers who lose out as a result of the changes will have their salaries safeguarded until 2008.
But while schools have made cuts of up to 10 in the number of posts attracting allowances, only five will have a lower staffing budget after the end of the safeguarding period.
Steve Sinnott, NUT general secretary, said: "This will have a severe impact on the upper range of the upper pay spine."
Chris Keates, general secretary of the NASUWT, one of the unions who agreed the changes with the Government, said heads who have not set aside money to allow teachers to progress on the upper pay spine would get into difficulties.
"The whole idea of this process is that it gives a number of career paths for teachers and allows them to increase their salary and stay in the classroom. Guidance makes clear that heads can't use funding as a reason not to move teachers onto UPS3."