Its review says local authorities have to take their share of the blame for delays to the project to rebuild or refurbish every secondary school in the country by 2020.
It also said councils initially paid “insufficient attention” to how the complicated partnerships required for the schools building programme would function and that this had contributed to projects falling behind schedule.
Renewing the Secondary School Estate said: “It took six months longer on average than initial estimates to procure a local education partnership.
“It also took local authorities 18 months to develop strategic plans, compared with initial expectations of just over six months.”
The NAO said that while the bulk of the “16 to 23%” increase in costs was due to expanding the scope of the programme, around one-third of the hike was the result of a failure to correctly predict the effects of building-industry inflation.
Shadow children’s secretary Michael Gove said the government’s handling of the project was “shambolic”.
A DCSF spokesman said that the department had “always been upfront about the early delays” in the programme and had learnt lessons.
And a Partnerships for Schools spokeswoman said many of the report’s findings about BSF were positive. She was confident that the “vast majority” of schools would be finished by 2020.
“It is better that local authorities take slightly longer over the planning phase of the programme than stick slavishly to the timetable and create a partnership that is not fit for purpose,” he said.