The report concluded that the Department for Education was unprepared for the extra expense of rapidly accelerating the coalition's academy conversion plans.
In May 2010 there were 203 academies but by September 2012 around 2,309 schools had converted, representing a growth of 1,307%. The result is that now, 48% of secondary pupils attend academies.
The report says that the DfE had budgeted £7.3bn to set up and run academies between April 2010 and March 2012.
Officials were reportedly expecting some extra expenditure, to cover factors such as additional insurance, but were unprepared for the numbers of academies wanting to convert. In fact the total expenditure on academies amounted to £8.3bn - £1bn over budget.
A significant portion of the overspend, £350m, was paid to local authorities for temporary continued funding of places at non-academy schools, effectively double funding places while the new academies were being set up.
The report says that to fund the expansion and remain within overall spending limits, the DfE had to find the money from other budgets, including the main schools settlement.
Christine Blower, General Secretary of the National Union of
Teachers, said: "The National Audit Office report specifically warns against deeming the academies programme ‘value for money'. Unsurprising when 10% of the Department for Education's total budget has been expended on this project, with a staffing increase of 133% in those posts focusing on this work."
Blower labelled the expenditure "absurd", considering the economic conditions and many state schools being left to languish in a state of disrepair.
She also pointed to certain figures within the academy movement, such as academy super heads and insurance companies, who are profiting from the process at the public's expense.
In addition Blower cited some schools' perception of actually being "less free from bureaucracy" than they expected under the new system and a lack of transparency, with accountability being reduced to "an act of faith based on self-reporting."
Blower concluded: "Another 400 ‘forced' academies were announced last week, a further instalment in the saddening tale of coercion and bullying which has characterised some aspects of the academies programme.
"High quality teaching drives up standards, not academies. The Prime Minister and the Secretary of State should instead be investing in teachers and supporting all schools."