Figures disclosed in parliament revealed that the proportion of academy students taking GCSEs in courses including English Literature, history and individual sciences are outstripped by those at maintained schools.
In foreign languages and geography, entries from academies were more than a third lower than the average for maintained schools.
Opponents said the figures showed academies had abandoned non-compulsory academic subjects in favour of less challenging GCSEs and equivalent qualifications to boost their performance in league tables.
Academies, which are not subject to freedom of information laws, have faced calls to be more open over the curriculum they offer and the pay of staff.
The figures, based on exams taken last summer, came to light following a question in Parliament by Tristram Hunt, MP for Stoke-on-Trent central, and research by Civitas.
It follows data showing that academy pupils are awarded twice as many A* to C grades in non-GCSE qualifications as maintained schools, but two thirds as many of the equivalent GCSE grades.
Anastasia de Waal, Director of Education at Civitas, said: "Academies are supposed to be improving not impoverishing education, so to find that the proportion of academy students doing core academic subjects is much lower than average makes a mockery out of the notion that academies are exemplary.
"Withdrawing academic GCSEs and replacing them with weak substitutes has been great for academies’ league table position but hugely detrimental to the already often limited opportunities available to the young people they serve."
In academies, just 21 per cent of pupils took a GCSE exam in history and 17 per cent in geography last year, compared with 30 per cent and 26 per cent respectively in maintained schools.
Academies entered just eight per cent of pupils for individual exams in physics and nine per cent in chemistry and biology, compared with 12 per cent for each of the three subjects in maintained schools.
The biggest difference was in foreign languages, where just 26 per cent of academy pupils were entered for a GCSE compared with 41 per cent in all maintained schools.
Dr Mary Bousted, general secretary of the Association of Teachers and Lecturers union, said: "There is nothing wrong with academies devising a curriculum which will get the children to school and get them wanting to learn.
"But the difficulty is when the qualifications are a spurious equivalent to a GCSE, which are widely used to push up the GCSE results of academies to show that they are getting much better results than state schools."
A spokesperson for the Department for Education said: "The fact is that Academies are working - academies have been over three times more likely to be rated outstanding by Ofsted than other state schools, since their new tougher inspection regime was introduced, while half as many Academies are judged inadequate.
“Ministers are clear that young people should be 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."
--=By Nick Collins,16 Jul 2010