The number of state secondaries in England said to be underperforming has more than doubled amid exam changes.
Some 330 schools failed to get 40% of pupils gaining five good GCSEs including English and maths, and making the expected progress.
This rise, from 154 last year, comes after ministers toughened exams and banned re-sits and some vocational qualifications from school tables.
Meanwhile scores of top private schools have ended up bottom of the tables.
These include renowned schools such as Eton, Harrow, Winchester and St Paul’s Boys’.
This is due to the fact that, in some independent schools, pupils have continued to be entered for unregulated versions of qualifications, such as IGCSEs.
The changes have prompted claims from state and private school heads alike that the league tables are a “nonsense” and the results therein are not comparable with previous years.
School performance data released by the Department for Education – based on last summer’s exam results – shows that on average 56.6% of pupils in state schools in England achieved the benchmark of five good GCSEs including maths and English.
This is a decline of four percentage points on 2013, when 60.6% of pupils in state schools reached this benchmark.
The dip in the overall performance of schools comes in the wake of government changes designed to make exams more academically rigorous.
From this year, only a pupil’s first attempt at a qualification is included for league table purposes. This was aimed at ending the practice of schools entering pupils for re-sits to boost their ranking.
The list of qualifications included has also been restricted to those the government says are of the highest academic quality, and the number of non-GCSEs counting has been capped at two.
The school with the best GCSE results was Pate’s Grammar School in Cheltenham, Gloucestershire.
Education Secretary Nicky Morgan said: “For too long pupils were offered courses of no value to them and schools felt pressured to enter young people for exams before they were ready.
“By stripping out thousands of poor quality qualifications and removing re-sits from tables, some schools have seen changes in their standings.
“But fundamentally young people’s achievement matters more than being able to trumpet ever higher grades.”
But for some schools, the confusion over which IGCSEs count towards the league tables has cast a cloud over this year’s rankings.
The IGCSE – or international GCSE – is sat by candidates overseas, but has long been favoured by many private schools and some leading state schools 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.
Many leading schools – such as Cheltenham Ladies’ College, Eton, Harrow, Winchester, Oundle and Marlborough – are now reported as having 0% of pupils attaining the government’s benchmark of five GCSEs at grades A*-C including maths and English.
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 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,” he said.
“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.”
Brian Lightman, general secretary of the Association of School and College Leaders (ASCL), 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.
“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 said some state schools had been “caught unawares”, adding many were already unhappy with the way their results had been presented in government data.
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 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 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.”