Scores of England's top private secondaries expect to be at the bottom of the school league tables, following confusion over International GCSEs.
School leaders dismissed this year's tables as a "nonsense", with many schools "caught unawares" by a shift in which qualifications are recognised.
It centres on the phasing out of unaccredited IGCSEs from the tables.
The government said it had made important changes to a system that had rewarded the wrong outcomes.
The IGCSE is sat by candidates overseas, but has also long been favoured by many private schools and some leading state schools in England as a more rigorous assessment.
They were once heavily promoted by the coalition government as a way of increasing rigour in the exams system, but now it wants pupils to take the new "more ambitious" GCSEs currently being phased into schools.
Richard Harman, chairman of the Headmasters' and Headmistresses' Conference (HMC), which represents many leading independent schools, said the decision to drop IGCSEs made a "nonsense" of the league tables.
"Several of the UK's most highly performing independent schools and others offering this excellent qualification will now appear to be bottom of the class in the government's rankings.
"This obviously absurd situation creates further confusion for parents as they cannot compare schools' performance accurately and transparently.
"Many HMC schools will continue to offer the IGCSE, as experience tells us it is rigorous and offers a good basis for sixth form study."
But Graham Stuart, chair of the Commons Education Select Committee, said the publication of performance data was aimed at state schools, not fee-paying ones.
"They're not designed to serve independent schools. They are designed to create a benchmark for state schools."
Brian Lightman, general secretary of the Association of School and College leaders, said "quite a few schools have fallen foul" of the various changes to school league tables "by continuing with exams that don't count".
"In spite of this, the children themselves have received a good set of qualifications," he added.
"This calls into question the validity of the performance tables, and the government has promoted these qualifications [IGCSES] heavily in the early years of the coalition, but now they have decided that they want everyone to do the new GCSEs.
"Lots of independent schools are carrying on with IGCSEs and have no intention of stopping - their reputation goes beyond the league tables."
He added that some state schools had been "caught unawares", adding that many were already unhappy with the way their results had been presented in government data.
Russell Hobby, general secretary of the National Association of Head Teachers, told the BBC's Today programme the removal of IGCSEs and other qualifications mean year-by-year statistics are "not comparable".
A spokesman for the Department for Education said: "As part of our plan for education we are making GCSEs more ambitious and putting them on a par with the best in the world, to prepare pupils for life in modern Britain.
"We have made important changes to a system that rewarded the wrong outcomes.
"We have stripped out qualifications that were of little value and are making sure pupils take exams when they are ready, not before.
"The changes may result in some variation across all types of schools, ensuring they are held to account for the right outcomes.
"We issued guidance to all schools on this."
The DfE added that in some independent schools, pupils had continued to be entered for unregulated qualifications that did not count in performance measures, such as IGCSEs, and they had not been moved across to the regulated certificate versions.
"The effect of this has been enhanced in 2013-14 by the final group of unregulated IGCSEs reaching the end of their grace period and not being included in results."