John Dunford, general secretary of the Secondary Heads Association, has written to Education Secretary David Blunkett complaining that the new "value-added" mechanism will damage the reputation of good schools.
SHA already has angry letters from schools upset at being branded failures, despite improvements in their results. The new analysis, called the Performance Indicator, is planned for this year's exam league tables in November and will compare the progress between key stage 3 results and GCSEs two years later.
It will replace the year-on-year comparison of GCSE results introduced last year. But secondary heads believe it will distort schools' performance. Mr Dunford says that key stage 3 test results are not reliable and that the Performance Indicator penalises schools which limit the number of GCSE entries and those which do well in key stage 3 tests.
He contends that the indicator is statistically flawed because key stage 3 results are based on all pupils while GCSE results are based only on candidates, and because a school's make-up changes between the ages of 14 and 16.