Academies are significantly more likely than other secondaries with comparative intakes to fail on the Government's new GCSE achievement measure, a TES analysis reveals.
No pupils gained the English Baccalaureate in 31 per cent of the academies that entered pupils for GCSEs and their "equivalents" last year.
But only 17 per cent of non-academy comprehensives and secondary moderns with the same proportions of pupils on free school meals and with special educational needs completely failed to score on the EBac.
The measure - which requires pupils to gain GCSEs or IGCSEs of at least grade C in English, two sciences, maths, history or geography and a language - is the first to shed official light on how many schools are climbing league tables without core academic GCSEs.
The analysis suggests academies have made greater use of equivalent qualifications, dubbed "pseudo-vocational" by critics, than other secondaries with "challenging" intakes.
It casts doubt on ministers' claims that academy GCSE results have been improving faster than the national rate - a central justification of the vast expansion of the EBac.
Anastasia de Waal, education director of think-tank Civitas, said: "If we are really interested in evidence-based policy then this information is incredibly important. Kids from already deprived backgrounds are being further deprived of important courses."
Ministers argued this month that an academic education should be available for all and that the EBac was a "rigorous measure of success in academically stretching exams".
But in 58 of the 187 academies where pupils sat GCSEs last year, no EBacs were achieved. Only six academies saw more than one-third of pupils achieve an EBac and five of those were recently converted independent schools.
Just 8 per cent of non-academy comprehensives and secondary moderns registered a complete failure on the EBac. But that figure includes schools with very advantaged intakes.
For a fair comparison, The TES removed non-academies with lower proportions of pupils eligible for free school meals (FSM) until their average FSM measure matched the 29.1 per cent average of the academies.
The resulting group of 970 comprehensives and secondary moderns had a slightly higher average proportion of key stage 4 pupils with special educational needs than the academies. But only 169 of them completely failed on the EBac - a significantly lower proportion than the academies that scored zero.
Academy heads argue it is unfair to judge them retrospectively on the EBac because it did not exist when pupils sat their GCSEs.
The Independent Academies Association also says the measure will only be the "right mix" for some pupils and that "practical students" would be better suited to a "technical Baccalaureate". But the Anti-Academies Alliance said it showed their success was "built on sand".
Many academies have been reluctant to reveal details of their exam results, hailed by the Commons Public Accounts Committee this week as "rapid academic improvements".
When Civitas surveyed academy heads in 2009, only 55 per cent believed breakdowns of their exam results should be published. Government figures obtained since by Civitas, Labour MP Tristram Hunt and The TES show that in 2009, nearly half of academy A*-C GCSE grades actually came from "equivalent" vocational qualifications.
Further official figures obtained last year may shed light on the poor EBac performance, showing that in 2009 only 17 per cent of academy pupils were entered for a geography GCSE, 20.9 per cent for history and 26.1 per cent for a modern foreign language.
A Department for Education spokeswoman said the figures were "not surprising" because academies replaced "low-performing" schools.
- Original headline: Academies outperformed on EBac by other `challenging' secondaries