Chris Woodhead, the Chief Inspector of Schools, said heads were largely to blame for the differences revealed in the report, which is the most comprehensive review of secondary education ever published.
But headteachers said that his inspectors were at fault for pillorying struggling schools and preventing them from attracting good staff.
The report, from the Office for Standards in Education, covers all 3,600 secondary schools in England and notes that the gap between the GCSE scores of the top 10 per cent of schools and those at the bottom widened between 1992 and 1996.
Mr Woodhead said: "Schools that have headteachers focusing on their school's problems and moving them on are making progress. Those which do not are not. Leadership is good in three out of four schools but some senior managers do not really know what is happening in the classroom."
Some heads, according to the report, are frightened to confront bad teachers. It says that two in five secondary schools are consistently good. But one school in ten is poor. Two out of five pupils lack the basic skills they need, and the proportion leaving without a single qualification is rising - up to one in 14. And the proportion of schools where behaviour is good has fallen.
Standards for schools with similar backgrounds vary widely. Among those with a fifth of pupils on free meals, some are doing more than twice as well as others at GCSE.
Stephen Byers, the school standards minister, welcomed the progress which has been made, but insisted that some schools could do better. Good education "should be a right not a lottery", he said.
John Sutton, general secretary of the Secondary Heads' Association, said that Government policies, not his members, were to blame for the increasing gap between schools.
"League tables, naming and shaming of schools coupled with enhanced parental choice, have inevitably meant that favoured schools have found it easier to produce improvements. Because it has failed to get the right balance of pressure and support for schools in difficulties, Ofsted is part of the problem rather than the solution."
Roger Coxon, head of Handsworth Wood Boys' School in Birmingham, a failing school which will close this summer, told BBC Radio 4's Today programme: "Ofsted is about putting pressure on people to make sure they do it better. That is unrealistic. If someone starts haranguing you, are you going to do it better?"
Urban schools with many pupils from poor backgrounds face an uphill struggle, the report acknowledges. Among the 100 schools with the highest proportion of pupils on free school meals, only three - all girls' schools - reached the national average score for GCSE.
Though teaching generally is improving, too many teachers are still failing to cater for pupils of all abilities. In particular, the brightest pupils often suffer because teachers give them work which is too easy.
The report offers only qualified support for the Prime Minister's call for more "setting" - grouping pupils according to ability in particular subjects. Those in top and bottom sets do better than those in middle sets and in mixed-ability groups.
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