They were languishing in 472 schools named on a Government hit-list for failing to hit basic GCSE targets.
Thirty-one of the schools - where fewer than 30 per cent of pupils get five good grades, including English and maths - have already closed.
A total of 1.6m were also taught in secondaries where fewer than half of children got good GCSEs last summer.
The Schools Secretary admitted that headteachers and governors of schools in some deprived areas were "badly letting children down".
School-by-school results also show:
*32 of the Government's flagship academies are among the bottom 440 schools, which may be closed unless they improve
*132 of those on the hit-list saw results decline
*Hundreds of secondaries are still shunning the three-Rs by promoting "soft" subjects
*A quarter of pupils in the toughest schools are classed as habitual truants after skipping the equivalent of one day a week
*Grammar schools are outstripping the private sector by a record margin in corresponding A-level rankings
Mr Balls said: "An excuses culture is still there in some communities and that's unacceptable.
"In a school where you have a head teacher or governing body that says 'It can't be done, leave us alone, this is the best kids can do' that attitude is totally unacceptable and if it requires change we can step in."
The tables chart standards in around 4,000 state and independent schools.
In the past, they were ranked by the number of pupils passing five GCSEs - or equivalent vocational courses - in any subject.
Critics claimed they could boost scores by focusing on "easier" courses such as computing, media studies and dance.
Now pupils have to gain at least a C in the core subjects of English and maths to be counted.
An analysis shows how the results of many state schools have collapsed under the new-style rankings.
Joseph Ruston Technology College in Lincolnshire - which closed last summer - saw its results plummet from 99 per cent to just 35 per cent.
At Stockland Green School in Birmingham, 77 per cent of pupils gained five good grades, but it fell to 15 per cent when English and maths was added.
In all, more than 900 schools - almost one in three - dropped by 20 per cent between the two marks.
It underlined the extent to which schools were failing to promote the basics.
Meanwhile, A-level results - which are included alongside GCSEs in official rankings - show the average grammar pupil achieved higher results than those in fee-paying schools.
Each pupil gained 73 points more than their privately-educated peers - equivalent to a third of an A grade.
Teenagers accrue A-level points in a system operated by the Universities and Colleges Admissions Service (UCAS) to govern entry to higher education. The higher marks could be enough to propel some students onto the most sought-after courses.