Both the National Association of Head Teachers and the Secondary Heads' Association are concerned that the new measure will give value added a bad name.
The Government is describing the new indicator as a school progress measure - not full value added. It will be based on the average progress made by a whole year group between key stage 3 tests and GCSE exams.
Future value-added measures will use progress made by individual pupils between key stages, a more accurate measure that also reduces the potential for skewed results from schools with high pupil turnover.
The two associations say many heads believe the 1996 KS3 test data is unreliable. David Hart, the NAHT's general secretary, has written to Education Secretary David Blunkett saying it is wrong to "jump the gun with an even more untried arrangement a year early" when a new and untried value-added system is being consulted on for 1999 by the Qualifications and Curriculum Authority.
"What possible purpose can be gained by moving, for just one year, to an interim and questionable value-added approach for KS3 to GCSEGNVQ against which it will not be legitimate to compare future value-added results?" he asked.
John Dunford, SHA's general secretary-elect, said: "We are furious. We believe value added is the acceptable face of inter-school comparison, but this will give value added a bad name, because the 1996 KS3 tests in English have no credibility. It is possible that in due course the national curriculum tests might bed down and achieve a sufficiently reliable reputation for us to be able to say that it is a reasonable indicator."
Both associations are also concerned about plans to average the levels attained at KS3 in English, maths and science in each school, But David Hawker, the QCA's head of curriculum and assessment, said this would be accurate enough for value added.
This year's performance measure could prove adequate for most schools, except those with a high turnover of pupils in the relevant age group.
"The better way of doing value added is looking at the progress made by individual pupils. We are setting up various exercises to do that," Mr Hawker said. "We would all want to get it right first time. But it would not have been possible to do that this year because the database is not yet well enough developed to produce comprehensive, pupil-matched data for value-added tables."
A report on the QCA's consultations on value added will be with ministers by the end of July. Full value-added measures will be introduced to secondary performance tables in 1999 or 2000.
A DFEEspokeswoman said: "The progress measure is an important step towards publication of full value-added measures in the longer term. If we are to go ahead with a progress measure, we must ensure comparability across the country. These measures must come from national curriculum data and we are satisfied that the 1996 key stage 3 data is fit and useful for this purpose."