Five hundred secondary schools in England did not meet the government's minimum target for GCSE attainment, the annual performance tables show.
Ministers unapologetically "raised the bar", saying the benchmark of five good grades must include English and maths.
They want a quarter of pupils in every school to manage this - but in almost a sixth of schools they did not.
Yet many do well on a new "value added" measure taking account of factors such as gender, ethnicity and deprivation.
The tables confirm that, across the country, 45.8% of pupils at the end of Key Stage 4 of the national curriculum attained the equivalent of five GCSEs at grade C or above including English and maths.
The director general of the British Chambers of Commerce, David Frost, said this figure was "shocking".
2006 SECONDARY TABLES
The tables, compiled by the Department for Education and Skills, provide a school-by-school breakdown of those national averages.
In 114 schools every pupil achieved the new English and maths benchmark - 34 of them state schools, the rest in the independent sector.
The best, on the basis of the average points each pupil attained, was Chelmsford County High School for Girls in Essex.
The 119 pupils averaged 738 points in their exams - equivalent to more than 12 A* grades.
The worst was Temple School near Rochester in Kent, where only 2% of the pupils managed five good grades including English and maths.
Average points among the 125 pupils there were 235.
"We knew we had made a large improvement but we didn't really know we would be the most improved"
But many well-known and high-performing independent schools such as Rugby, Harrow, Dulwich College and Uppingham also appear to do badly.
Their pupils sit International GCSEs in English and maths, which they regard as more challenging - but which are not counted in the official tables, much to their annoyance.
There has been a "value added" progress measure for some years - comparing pupils' attainment with that of all other pupils with similar prior attainment.
"There should be no hiding place for underperforming and coasting schools "
That has now been "contextualised" to give a new CVA indicator, which factors in nine things reckoned to affect pupils' attainment, such as gender, special educational needs, ethnicity and local deprivation.
A complex calculation generates a predicted outcome for each pupil, based on the results of all similar pupils.
If their actual results are higher than predicted, the government says the school has had a positive impact - if lower, it has failed to fulfil their potential.
The best school on that basis was the Academy of St Francis of Assisi in Liverpool - the country's first inter-faith academy focusing on the environment.
'Not enough'
Schools Minister Jim Knight said including English and maths in the "gold standard" reflected the importance the government placed on equipping youngsters with "the basics".
He added: "There should be no hiding place for underperforming and coasting schools that fail to make a significant positive impact on their pupil's progress."
Shadow education secretary David Willetts said the new benchmark did not go far enough: the basics should include the sciences, history and modern languages.
"This is what every pupil is entitled to and deserves. Currently, too few pupils are being given this opportunity."
Liberal Democrat education spokeswoman Sarah Teather said the new benchmark highlighted "the perverse incentives" created for schools by the league tables.
"The answer to this problem is not to add more categories but to scrap them all together," she added.
The general secretary of the NASUWT teachers' union, Chris Keates, said the "unnecessary, divisive and demoralising annual ritual" of the tables encouraged competition between schools at a time when the government was promoting collaboration.
The third major change this year is that A-level results now include many vocational qualifications, as was done with the GCSE-level results some years ago.
This necessitated a new points score, devised by the Qualifications and Curriculum Authority. An A-level at grade A is worth 270 points.
The top school was Colchester Royal Grammar, whose students averaged 1,258 points each.
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