Warwick Mansell and Graeme Paton Academies are costing the taxpayer up to pound;50 million each, The TES can reveal.
The two most expensive academies each received more than pound;40m in public funds in two years, in building, start-up and running costs, an analysis of the accounts of the first 17 schools shows. A further eight have cost at least pound;25m.
As well as building costs of up to pound;35m, the accounts reveal that "start-up" overheads for eight of the new schools were more than Pounds 1m.
Overheads at three academies ran to more than pound;2m.
The revelations will pile more pressure on the Government. They emerge as a new report says academies are a "high-risk" investment for wealthy donors interested in education (see story, right).
However, academy heads have strongly defended their costs. Sir Michael Wilshaw, principal of Mossbourne Community Academy, in Hackney, east London, said ministers should be praised for investing in inner-city areas."For the first time, these children are getting a fair crack of the whip," he said Bexley business academy emerges as the most expensive of the new schools.
It took pound;46.3m in public-sector grants between 2001-4.
The south London academy, sponsored by the property developer Sir David Garrard, received pound;12.5m in 2003-4, pound;23.1m in 2002-3 and Pounds 10.6m in 2001-2. Of this, pound;35m was spent on building work.
Costs for the 2004-6 academic years are likely to bring the total bill above pound;50m.
Sir David has so far contributed pound;2m, the accounts show.
At West London academy, which opened in 2003, the total bill to the taxpayer for the three-year period 2002-5 is pound;45.9m.
Mossbourne community academy, in Hackney, east London, received pound;29m in government grants in 2003-5, despite only educating 210 pupils in 2004.
Building costs for each academy were originally billed as pound;10m. The schools also receive the same level of per-pupil funding as they would have done as a community school.
However, the TES analysis reveals the amount allocated to the new schools for "start-up costs", including funding for project management and some extra staffing. This is in addition to annual revenue funding and represents an extra cost.
West London academy said that its pound;7.5 million running costs were to be expected of a school of its size. Ealing council said pound;5.1 million had been paid to West London academy for the building of a council-run special school on the academy site. This is listed in the academy's accounts as income.
A Department for Education and Skills spokesman said: "Academies are built to similar building specifications as other state schools. The average cost of a new secondary school with 1,300 pupils including a sixth form in a high-cost inner-city area is pound;25 to 30 million.
"The average cost of an academy, of this size and location is similarly Pounds 25-30 million. And their revenue funding is also comparable to maintained schools in the same area."