Pay bills for senior staff have increased at most schools as a result of a new allowances system meant to free up cash to pay for the same teachers'
progression up the salary scale.
Welsh headteachers have until March 31 to restructure their staff to take into account teaching and learning responsibility payments (TLRs), following the abolition of management allowances.
But some staff who have lost management allowances and missed out on TLRs could now miss a pound;1,200 move up the upper pay scale because heads have overspent their pay bill.
A TES survey shows salary bills in almost nine out of 10 secondaries in England will increase as a result of TLRs, despite schools cutting the number of promoted posts. English heads had to produce new staffing structures by December 31. Heads reported their schools would be up to pound;100,000 a year worse off as a result of the changes.
Savings from TLRs were supposed to pay for "the substantial majority" of senior teachers on UPS2 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 support staff employed to free teachers from administration, said heads.
Fifty-eight schools responded to the TESsurvey, sent to a representative sample of 200 secondaries.