Less than half of academies' "GCSE" passes are made up of academic GCSEs, according to new government figures.
The statistics also show that the state-funded independents make twice as much use of vocational and other non-GCSE "equivalent" qualifications as other state secondaries.
The figures, published in response to parliamentary questions, challenge the idea that academies outperform conventional schools.
Critics say they are a blow to the credibility of the planned expansion of the academies programme.
Ministers have justified the policy by claiming that average academy GCSE performance is increasing at twice the rate of other secondaries.
But that figure is based on the league table measures that include "equivalent" qualifications.
The Government has revealed that only 49 per cent of academies' GCSE or equivalent A*-C grades were made up of academic GCSEs last year, compared with 73 per cent for other state schools.
Anastasia de Waal, education director at think-tank Civitas, said: "Academies are replacing academic subjects with so-called equivalents of extremely questionable value.
"The ultimate concern is that the already deprived are being deprived of academic learning and that un-checked this is set to continue much further."
Applied GCSEs made up 3 per cent of academies' A*-C passes, with the other 48 per cent made of "equivalent" qualifications, including BTechs, OCR Nationals, basic, key and functional skills, NVQs and VRQs.
Mainstream state secondaries made half as much use of these alternatives - only 24 per cent of their A*-C passes.
Tristram Hunt, Labour MP and historian, said the news was particularly embarrassing for Conservative ministers because they had continually emphasised the importance of a strictly academic education in "hard" subjects.
Their own figures showed this was much less likely to be offered in many of the academies they were promoting as the flagship model of reform.
"This begins to confirm our initial fears that in many academies history, geography and other academic subjects are falling behind," said Dr Hunt, who tabled the parliamentary questions drafted by The TES.
"It is of real concern that the Government seems about to depart on a policy without gathering the empirical evidence of what is going on in schools."
The latest government figures follow another set published by The TES last week which showed that individual academies were, proportionately, much more likely to appear among the schools making heavy use of non-GCSEs.
A Department for Education spokesman said: "Results and inspection reports show that academies are working.
"Based on the national standard upon which all schools are measured, academies' GCSE results are increasing twice as fast as the national average.
"It is very important that young people are entered for the qualifications that are in their best interests rather than being entered for exams simply to boost the league table position of the school."
- Original headline: Less than 50% of academies' `GCSE' passes are academic subjects