Headteachers have complained that the measure is "so flawed as to be virtually useless". David Hart, general secretary of the National Association of Head Teachers, has sent a four-page letter to the Education Secretary David Blunkett listing his concerns.
The NAHT's rival union, the Secondary Heads Association has already expressed its disquiet, saying that good schools have been wrongly condemned as making little progress.
The new measure compares a school's performance at key stage 3 in 1996 with this year's GCSE results, to produce gradings ranging from A ( most progress) to E. Schools have already been notified of their category.
Mr Hart, who says he has received complaints from around a dozen headteachers, said that so-called "D-grade" schools include:
* a grammar school with 41 per cent of its GCSE candidates achieving A* and A grades; * a comprehensive with 70 per cent of its 15-year-olds achieving five or more A to C grades; * a comprehensive which has improved its five A-C grade pass rate from 42 to 62 per cent.
In his letter, Mr Hart questions the reliability of KS3 statistics, and the validity of compounding KS3 results for maths, English and science tests.
Schools that performed well at KS3 would be penalised because it would be harder to "add value" to already good results, he writes. And the system used for measuring GCSEGNVQ performance (based on points scores) would favour those schools which enter pupils for more exams.
"In practical terms, this means that if pupils at school X take 11 subjects, with an average of a B grade each (average subject score equals six points), they contribute 66 points each," he writes.
"If at school Y, the pupils take eight subjects (and do a Duke of Edinburgh award and study a broader curriculum), they can 'only' contribute 64 points each, even if they achieve an A in all eight subjects (average subject score equals eight points). This would be enough to put school Y in value-added band D and its rival school X in band C.
"It appears the government regards 880 runs in 11 innings as a better performance than 800 runs in eight innings."
The new progress measure may be an unrepeated "one-off." The Qualifications and Curriculum Authority is piloting a more comprehensive system which could be introduced from 1999 or 2000.