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 secondaries 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, carried out by the Press Association, also reveals that a child's chances of attending a decent school 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 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 schools did not meet the minimum benchmarks. There are around 3,300 state secondaries in England.
Of those that did not make the benchmark, 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".
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.
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 were free schools - a key element of Conservative education reforms.
These 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 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, 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 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 secondaries - around 7.3% of the secondary school population, the data reveals. This is down from last year, when the figure was 274,351.
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).
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, at 47.7%, and Nottingham where 35.7%.
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 with 2010.
Of those schools which 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.
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 under-performance so every child fulfils their potential."
Russell Hobby, general secretary of the National Union of Head Teachers, said: "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."
Shadow education secretary Lucy Powell said: "While I celebrate those schools that are performing well and I applaud teachers and others working tirelessly to get the grades, it is deeply concerning that a quarter of a million pupils are in failing secondary schools, and alarmingly the attainment gap between disadvantaged pupils and their peers has grown for the third year in a row.
"The attainment gap is now bigger than when David Cameron took office in 2010."