All schools are supposed to publish new staffing structures by the end of December. But The TES has learned that a panel of heads and senior teachers, appointed by the Government to monitor the impact of its policies, has written to ministers saying the deadline could be impossible to meet.
Any delay would cause chaos as schools are supposed to partially fund pay rises for experienced teachers from the savings they make in replacing management allowances with teaching and learning responsibility payments (TLRs).
The problem will mean a difficult autumn for Ruth Kelly, if she survives the election as Education Secretary, or for David Miliband, already being touted in Government circles as her successor.
Next term heads will also have to cope with implementing teacher planning, preparation and assessment time, that many say they cannot afford.
This week Mick Brookes, who takes over as National Association of Head Teachers general secretary in September, upped the stakes with a call for enough funding for teachers, rather than support staff, to provide the 10 per cent PPA cover.
In its letter to Ms Kelly this month, the implementation review unit calls for her to assess how long it will take the average primary and secondary to work out how to introduce TLRs.
Chris Nicholls, the unit's chair, said: "We said that if the assessment shows there is quite a lot of work involved in this, and I think it might do, then there is a case for delay.
"September 2006 may make a more rational date."
The new system, agreed between the Government, employers and most of the teaching unions, and which is supposed to be phased in by the end of 2008, is already controversial, as it will mean pay cuts for thousands of teachers.
Last week Nigel Middleton, a director of Head Support pay and conditions consultancy, called for a year's delay, saying the Government could face strikes and headteachers leaving the profession if it failed to act.
Stephen Twigg, school standards minister, said the Government was working very closely with unions and he was confident that they could make the new system work.