A hard-hitting report called for earlier intervention by inspectors and local authorities to turn round failing schools, and warned that without better support many more would be forced to close.
Almost one in four secondaries and one in 25 primaries are identified as poorly performing. Among them these schools educate one in eight pupils.
They include secondaries identified as coasting by the Department for Education and Skills, and schools which have been failed by Ofsted or given notice to improve as a result of serious weaknesses or underachievement.
Angela Hands, the NAO report's author, said if the same coasting criteria were applied to primary schools, the figure would rise to well over 1 million pupils.
Taxpayers spend about pound;1 billion each year supporting and replacing failing or at risk schools.
It can cost pound;500,000 to turn round a failing large secondary, but this is dwarfed by the average pound;2.2m cost of a Fresh Start school and the Pounds 27m it takes to build one of the Government's academies.
While the report praised the impact of the much-criticised Fresh Start initiative, it said it was too early to assess whether academies offer value for money.
The Government's white paper, published in October, promised to close schools placed in special measures within 12 months unless they show significant progress.
More than 1,500 schools remain poor performers, with most suffering from a combination of weak leadership, poor teaching and lack of support from their local authority.
The NAO called on the Government to tackle the growing shortage of heads and remove the barriers that discourage senior teachers from becoming heads.
It questioned whether the Government's model of superheads, each running more than one school, will raise standards.
The watchdog welcomed the recent reduction in the maximum gap between inspections from six to three years. But it called on Ofsted to visit schools at risk of failure even more frequently.
This could be balanced by less frequent visits to schools with a strong culture of self-improvement, the report said. Ofsted is already committed to consulting on whether to introduce such a system from September.
Fewer than one in 10 schools entering special measures recovers within 12 months, and some take more than four years. More positively, two-thirds have made reasonable progress within 12 months and 85 per cent recover within two years, the report said. Two years after coming out of special measures, most schools are good or better.
The spending watchdog said that the number of poorly-performing schools has declined in recent years. The number of schools in special measures has fallen by half since 1998, and the number of secondaries where fewer than 20 per cent of pupils gain at least five A*-C grade GCSEs has dropped by more than 75 per cent. But it reported that 40 per cent of schools which came out of special measures between 1995 and 1997 have since been closed.
Sir John Bourn, Comptroller and Auditor General, said: "The falling numbers of poorly-performing schools are welcome, but it is unacceptable for any school to carry on providing a poor education over a period that can take up a large part of a child's school career and deprive them of future prospects and opportunity."
Jacqui Smith, schools minister, said: "We have more than halved the number of failing schools from 515 to 242, but this is still 242 too many."
Edward Leigh, Conservative MP and chair of the Commons public accounts committee, said: "It is tragic that so many pupils are still not getting the education they deserve."
Teachers' leaders were critical of the report, describing it as flawed.
Chris Keates, NASUWT general secretary, said it concentrated on the tiny minority who have difficulties rather than the majority who succeed.
FIVE WAYS TO SAVE A SCHOOL
* Improve school leadership: "Two-thirds of schools that recover after an adverse inspection change their headteacher."
* Improve teaching standards: "Teaching quality can be improved by providing better assessment and coaching of teachers, but sometimes weak teachers have to leave."
* Better management of pupil behaviour: "Most headteachers of recovered schools believe that initiatives to improve behaviour contributed to their school's recovery."
* Collaboration with other schools: "Around half of schools in our survey benefited from the support of nearby schools and some others would have liked support."
* Fresh Start: "As well as getting extra funding , under this programme schools have changed their identity, their governing body and some or all staff."