More than a quarter of a million children are not getting a decent education, including pupils at three of the Government's flagship free schools.
New figures show that hundreds of state secondary schools fell below the Government's floor targets after failing to ensure that enough pupils gained five good GCSE grades and made sufficient progress in English and maths.
An analysis of the data, conducted by the Press Association, also reveals that a child's chances of attending a decent school still depend heavily on where they live, with 10 or more under-performing secondaries in some areas, and none in others.
Schools Minister Nick Gibb said that the results, based on last summer's GCSE grades, show how far the nation has come in raising standards, but added that the Government will tackle the "pockets of persistent under-performance".
Overall, 329 state secondary schools in England did not meet the minimum benchmarks this year. Of these, 312 failed to ensure that at least 40% of their pupils gained at least five C grades at GCSE, including English and maths, and that students make good enough progress in these two core subjects.
The other 17 schools were among 327 schools that opted in to a new "Progress 8" performance measure, which looks at the progress of pupils across eight subjects and fell below a certain threshold for this target. From next year, all schools will be measured against "Progress 8".
The Department for Education (DfE) does not publish a list of schools falling below its floor targets but according to the Press Association's analysis, using the DfE's methodology for calculating under-performing schools, three of those falling below the benchmark this year were free schools - a key part of Conservative education reforms.
These schools are: Robert Owen Academy in Hereford, Saxmundham Free School in Suffolk and St Michael's Catholic Secondary School in Camborne, Cornwall, which was the only state secondary school to fall below the floor standard in the county.
A total of 188 under-performing schools are academies, the analysis shows, while 50 are council-run schools, 45 are foundation schools, 14 are voluntary-aided and the others include university technical colleges, studio schools and further education colleges catering to 14 to 16-year-olds.
A DfE spokesman said that free schools are a key part of the Government's drive for educational excellence.
"The number of free schools with exam results is still too small to allow robust conclusions to be drawn," he insisted. "But under-performance at any school is unacceptable, and one of the strengths of the free schools programme is that when we spot failure we can act quickly."
In total, 250,955 youngsters are being taught in under-performing state secondary schools, the data reveals. This is down from last year, when around 274,351 were in schools considered failing.
The Press Association's analysis also shows that five areas have at least 10 under-performing schools. These are Kent (20 schools), Birmingham (11), Lancashire (11), Lincolnshire (10) and Northamptonshire (10).
At the other end of the scale, there were 41 areas with no failing schools.
Blackpool had the highest proportion of pupils at an under-performing school, with 48.6% of youngsters not getting a decent education. This was followed by Knowsley, where 47.7% of pupils are in a failing secondary, and Nottingham where 35.7% of youngsters are at schools under the floor targets.
The top school for GCSE results this year was The Blue Coat School, an academy in Liverpool, where all 124 students gained at least five C grades, including English and maths, and the average points score per pupil was 696.1.
The figures also show a rise in the numbers of youngsters taking the English Baccalaureate (EBacc) subjects of English, maths, science, a language and either history or geography, the DfE said, with nearly 88,000 more teenagers taking these academic subjects compared to 2010.
Of those schools who entered all their pupils for the EBacc one reported a 100% pass rate: the Henrietta Barnett School, an academy in Hampstead, north London, according to the analysis of the figures.
At A-level, more than half of exam entries are in traditional "facilitating subjects" - the subjects which universities and employers say help to keep teenagers' options open for the future, the DfE said.
It added that more girls are choosing science and maths A-levels, while more teenagers are continuing their studies past the age of 16.
Mr Gibb said: "The results show how far we have come in raising standards, but they also highlight where some pupils are still at risk of falling behind.
"We refuse to accept second best for any young person and we must now focus on extending opportunity for all. This government is giving all young people, irrespective of their background, a fair shot in life and we must not let up the pace of reform now.
"Through our focus on delivering educational excellence everywhere and the dedication of our schools, we will tackle those pockets of persistent underperformance so every child fulfils their potential."
Russell Hobby, general secretary of the National Union of Head Teachers, said: "Heads, staff and students have worked hard in every secondary school across the country to raise standards at a time of immense turmoil and disruption. We pay tribute to their dedication.
"Unfortunately there has been so much change that the national statistics generated by the government are increasingly dubious. Comparing one year with another, or one group of schools with another, is precarious at best when the very basis of measurement is different each time.
"The government must be careful what conclusions it draws.
"We desperately need stable measures of a stable examination system. We need this in order for data to become meaningful again. We need this, above all, so that schools and teachers can focus on teaching to the best of their ability rather than coping with constant change."
Schools that are considered under-performing face intervention, such as being turned into an academy or given a new sponsor to try to raise standards.