Figures released by the Department of Education and Skills show costs on the first 27 schools have spiralled from £608.7 million to £657.2 million - an 8 per cent hike.
Bottom of the class is Foster & Partners' Capital City Academy in Brent, where costs have mushroomed from £19.4 million to £27 million - or 39 per cent.
At the St Francis of Assisi Academy in Liverpool, where work is not yet completed, a £5 million overrun has been chalked up on an original budget of £15.4 million.
The National Union of Teachers says this is enough to build a secondary school and several primaries.
Only two academies have come in on budget - Macmillan Academy in Middlesbrough and the West London Academy in Ealing.
The embarrassing figures were obtained under the Freedom of Information Act by journalists in the capital.
Liberal Democrat shadow education secretary, Sarah Teather, called for the programme to be axed.
'The list of problems with the academies programme just gets longer,' she said. 'The costs are enormous, the results are inflated and the scheme should be halted.'
The National Union of Teachers said the academies initiative now smacked of the Wembley fiasco.
But a spokesman for the Department of Education and Skills said costs were tightly controlled. She conceded that budgets may alter during building and design 'for very good reasons'.