Results are better for new Academy schools
The National Audit Office (NAO) said many of the 203 schools which have already taken on the greater freedoms of academy status performed "impressively".
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Hide AdBut it warned these results cannot be assumed to be an accurate guide to how the model will perform when expanded to many more schools of different types, as the Government plans.
The NAO report said the rapid expansion of the scheme planned by Education Secretary Michael Gove will increase the scale of risks to value for money and will stretch the ability of his department and the Young People's Learning Agency to monitor a growing number of academy schools.
Mr Gove rushed through legislation to allow all schools to convert to independent academies within the state system. Some 142 schools will take on academy status this year, along with 74 approved under the previous Labour administration.
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Hide AdLabour claims many of the new academies opening under Mr Gove's scheme are more successful secondaries catering to relatively affluent communities, rather than the under-performing schools with disadvantaged pupils targeted under the previous government.
In Yorkshire, the region's academies achieved impressive exam results this summer, with several schools surpassing the national benchmark for GCSEs for the first time.
Amyas Morse, Auditor General at the NAO, said: "Many of the academies established so far are performing impressively in delivering the intended improvements.
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Hide Ad"It cannot be assumed, however, that academies' performance to date is an accurate predictor of how the model will perform when generalised more widely.
"Existing academies have been primarily about school improvement in deprived areas, while new academies will often be operating in very different educational and social settings."
Since 2002, the Department for Education has spent 3.2bn on the academies programme. This is mainly made up of core funding which would have gone to the schools whether they converted or not, but also includes 288m in start-up grants to newly-opened academies.
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Hide AdThe report found academies increased the rate of improvement in GCSE results when compared with trends in their predecessor schools, but cautioned that those in the future are "likely to include schools with a much wider range of attainment, and operating in very different community settings", and may not improve their performance in the same way.
While still below the national average, the proportion of pupils achieving five or more GCSEs at grade C or above was improving at a faster rate than in state schools with similar intakes.
A small number of academies made little progress, however, particularly when English and mathematics are taken into account, said the NAO.
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Hide AdAll schools have been expected to get at least 30 per cent of pupils to achieve five good grades – including English and maths but three academies in Yorkshire run by the same charity have failed to achieve this since opening in 2006.
Earlier this summer, Sheffield Park, Sheffield Springs and the Barnsley Academy all celebrated meeting the target.