Figures released yesterday showed that 57 per cent of all examination papers sat by independent school pupils received top grade passes, compared with 18 per cent nationally.
Jonathan Shephard, general secretary of the Independent Schools Council, described the results as outstanding. But he added that independent schools did have "concerns about the usefulness of some coursework and the GCSEs' capacity to stretch pupils at all levels of ability".
The top-performing private school was St Paul's School for Boys in London with a point score of 593.8 per candidate, the equivalent of 10 A* passes per pupil. The £13,500-a-year school is planning to ditch science GCSE in favour of the international GCSE, which is more like a traditional O-level. It may ditch maths too.
Martin Stephen, high master of St Paul's, said that the international GCSE offered pupils a better preparation for A-level. "We are moving to international GCSE in science, and maths is under consideration," he added.
The school's achievement failed to put it in top place overall in the country. It was beaten by six grammar schools and two comprehensive schools.
The school with the highest ranking was Thomas Telford, a City Technology College with a comprehensive intake, which achieved a point score of 744.5 per pupil - or almost 13 A* grades each - and topped the overall performance table for the fourth year in succession.
It has a policy of putting all its pupils in for at least one General National Vocational Qualification - deemed to be worth the equivalent of four GCSE passes - and 16 GCSEs in all.
The highest average number of subjects taken by pupils at any independent school was 11.
Meanwhile, the independent schools criticised the drift away from modern languages at GCSE.
The Government's decision to make the subject voluntary from the age of 14 has led to only 30 per cent of state schools still offering it as a compulsory subject for study at GCSE, compared with 97 per cent in the independent sector.
Mr Shephard said: "Some say French is globally in decline but it is lazy - and plain wrong - to assume that everyone in Europe can understand English if we shout loudly enough. This year there was even a small fall nationally in the number of entries at GCSE for Spanish, an increasingly important language, as well as dramatic falls in entries for French and German. This is potentially damaging for the UK's economic competitiveness."
Overall, the number of entries for languages was down 64,000, with French falling 14 per cent to 272,140, and German down 13.7 per cent to 105,268. Mr Shephard said the figures "should send alarm bells ringing out not just at the Department for Education and Skills but at the Department for Trade and Industry and the Treasury as well".
The number of independent schools opting out of the GCSE and taking the international exam as an alternative is expected to grow.
Geoff Lucas, secretary of the Headmasters' and Headmistresses' Conference, which represents the leading independent boys' schools, estimates that about 40 have either taken the decision to switch exams or are about to. Most were ditching maths because they believed the international exam was more rigorous.
Many have taken the decision in the wake of the refusal by Ruth Kelly, the Education Secretary, to back the reform of exams advocated by the former chief schools inspector Sir Mike Tomlinson. He recommended that GCSEs and A-levels be replaced by an overarching diploma.
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