David Blunkett, the Education and Employment Secretary, admitted the new index - called the progress measure - would have been unfair to many schools. It was designed to estimate how much "value" schools added by grading the GCSE scores of schools in relation to their overall key stage 3 test results.
Hundreds of headteachers complained to Mr Blunkett after receiving low grades despite topping GCSE tables. They protested that successful schools were at a disadvantage because their pupils achieved high test scores at 14.
Mr Blunkett is understood to have agreed that the index was not sufficiently reliable and would have discredited the development of "value-added" tables, which aim to measure progress.
He said: "We have listened to the concerns expressed by schools with good GCSE and KS3 results in particular and have decided that the most robust available measure of a school's improvement should remain the performance index this year. This will compare a school's achievement in GCSEs over the past three years."
The tables will now only record a tick for the 800 schools who would have received A or B under the new progress measure, showing they had higher-than-average GCSEs compared with their KS3 results.
David Hart, general secretary of the National Association of Head Teachers, said: "The Government's U-turn is an admission that our objections were right and the original plans were flawed. Although we would have preferred a complete withdrawal of the value-added measure, the substantial change is a victory for common sense." For the second year, the tables will focus on year-on-year improvements in raw GCSEs, but new this year is the average GCSE point score per pupil published alongside the five A*-C results.
Results of a value-added pilot will also be published as a supplement to this year's tables. The results of 200 schools have been used to calculate a "value added" measure based not on school averages but on the progress of individual GCSE pupils since their key stage 3 tests.