Terry Wrigley, an academic at Edinburgh university, said political pressure to improve results had resulted in schools steering pupils away from academic subjects and towards GNVQ equivalents.
"GNVQs do provide qualifications to pupils, but to use them as a device to claim that academies are working is completely flawed," he said.
In 2002 there was one GNVQ entry for every 10 pupils, compared with 12 for every 10 pupils last year, he said.
A spokeswoman for the Department for Education and Skills said that the findings were "complete nonsense".
"The National Audit Office report in February found GCSE performance in academies has improved compared with predecessor schools and it is improving in academies at a faster rate than in other types of schools,"