Heads have condemned ministers' attempt to press on with a "flawed" national scheme, due to start next year.
Their opposition has already led to the scrapping of the controversial "progress measure" which was due to appear in this week's performance tables.
Value-added measures aim to make comparisons between schools fairer by taking account of pupils' previous achievements.
They have widespread support in the education world. But the issue is so complex that officials plan to consult "People's Panels" - focus groups of members of the public - on how to make the tables less baffling for parents.
Starting next year, ministers planned to publish value-added scores for all schools.
These would have been based on a pilot scheme which features in this week's tables.
However, critics claim the calculations contain the same flaws as this year's controversial "progress measure" - intended to be a step towards full value-added.
Both schemes only measure progress between key stage 3 and GCSE. This is thought to disadvantage schools which raise 14-year-olds' achievement.
David Blunkett, the Education and Employment Secretary, eventually scrapped the progress measure, conceding it was unfair to many schools.
John Dunford, general secretary of the Secondary Heads Association, and David Hart, general secretary of the National Association of Head Teachers,have called on the Government to delay the publication of national value-added data until it can give an accurate measure of pupil progress between 11 and 16.
Current measures rely on data for 14 and 16-year-olds.
Mr Blunkett is keen to see the national publication of value-added information and will decide in the spring whether to extend the scheme in 1999.
The results of the pilot, which only measures progress between 14 and 16,were released by the DFEE this week alongside the school performance tables.
However, it may prove impossible to extend the pilot project in 1999 if national KS3 pupil data is incomplete. This could delay national publication until 2000.
Mr Dunford said: "The Government has just got to wait. It is important to get the measure right. David Blunkett admitted that the 14 to 16 progress measure was unfair to many schools, so this flawed pilot should not be extended. "
Headteachers and education statisticians want the Government to wait until key stage 2 data is available. But this year's KS2 results were the first to be collated in a suitable form for value-added, making a KS2 to GCSE comparision impossible before 2003.
A Department for Education and Employment spokesman said: "This is the first time that the DFEE has calculated and published a value-added measure on such a large scale.
"It is a pilot and although there were always good reasons for doing something in one way, it could often equally well have been done in another. Nonetheless the measures are statistically robust."
Harvey Goldstein, professor of statistical methods at the Institute of Education in London, condemned the pilot as "intellectually shoddy" and criticised the Government consultation as a "sham" which only asks for views on how the national data should be published, not on whether it should be.
The complete secondary school amp; college performance tables are published in a 40-page special section in today's TES.