A total of pound;425 million has been spent on the first 17 academies, due to open in September, rather than the pound;170m first budgeted. With numbers set to reach 50 by 2007, that bill could rise to pound;1.3 billion - equal to a third of the total capital budget for schools this year.
Official figures show rising land prices, inflation in the construction industry and ambitious designs have sent the average cost of each academy to more than pound;25m.
Neighbouring schools could be left to foot the bill for new academies after it emerged that the Government wants local authorities to use cash earmarked for school refurbishment to expand the programme.
Local authority leaders have accused civil servants of threatening to withdraw their councils' share of pound;2.2bn capital investment unless they agree to spend some of the cash on academies.
All 17 education authorities in the first wave of the Building Schools for the Future programme have to say whether they intend to use a proportion of the money to build an academy.
Ministers expect the programme to give every secondary school 21st century facilities within 10 to 15 years.
Senior government sources say that no authority will be forced to accept an academy against its will.
But Graham Lane, Local Government Association chair of education and leader of the London borough of Newham, one of the first-wave councils, insists Department for Education and Skills officials threatened to block Newham's bid unless it agreed to an academy.
Senior figures at two other councils confirmed they had also faced serious pressure.
Government guidelines say that no authority will be obliged to set up an academy provided that it produces an acceptable alternative to deal with failing schools.
Mr Lane said that government claims that authorities were free to choose were disingenuous. "There will be a tendency for authorities to have academies because they will fear losing the BSF money if they do not," he warned.
Current capital budgets for academies show that even the cheapest, the Manchester Academy, cost one-and-a-half times the pound;10m former Education Secretary David Blunkett indicated when he launched the scheme four years ago. The pound;2m that academies have each attracted in sponsorship amounts to just one-thirteenth of the total cost, compared to the fifth promised by Mr Blunkett.
The latest guidance on secondary school building costs, compiled in 2002 by the DfES, says the average total cost of building a new secondary should be around pound;14.6m.
The most expensive academy, the City of London academy in Southwark, cost pound;33.7m. Publication of the figures will draw protests from councils and teachers' organisations who have long feared their state-of-the-art facilities. Fears that most would select pupils by aptitude appear to be unfounded.
John Dunford, general secretary of the Secondary Heads Association, said he had written to Charles Clarke, the Education Secretary, to ask why the Government could not build cheaper academies and distribute some of the savings among other schools.
But a spokeswoman for the DfES said the cost of academies was broadly comparable with that of any new secondary school.
"The overall cost of academies has to be placed in context. They are typically larger than the average secondary school, they are exclusively in inner-city areas, and mainly replace existing open schools and usually require some temporary accommodation for the existing students," she said.
Analysis 18; leader 22; leadership 30