Four out of 10 council-run comprehensives need to do better, but the worst problems are concentrated in boys' schools, according to the research.
More than 10 per cent of the 119 boys' comprehensives "require substantial improvement," according to OFSTED inspectors. This compares with around 1 per cent of girls' comprehensives and 5 per cent nationally.
The research, obtained by The TES, comes amid mounting concern over boys' underachievement and a week before the publication of school performance tables.
Chris Woodhead, the chief inspector of schools, has said that under-achieving boys are "one of the most disturbing problems facing the education system".
Pat Mahony, professor of education at the Roehampton Institute, London said: "Today's under-achieving boy is tomorrow's unemployed youth. He is public burden number one, needing benefit in the world of global competition where governments want to get taxes down."
The OFSTED research, still in draft form, compares local authority, grant-maintained, mixed, boys' and girls' comprehensives over the past two years.
It shows that opted-out comprehensives out-perform their council counterparts - three-quarters are rated very good or good by the inspectors, compared with 60 per cent in the LEA sector.
More than 60 per cent of mixed schools and boys' comprehensives were high performers but girls' comprehensives did much better - almost 80 per cent getting good reports.
The disclosure of the serious problems in boys' schools is likely to cause concern. A book called Failing Boys launched this week and edited by academics at London's Institute of Education depicts the "fighting, fucking and football" culture of white, heterosexual, working-class boys.
It said macho lads went to great lengths to prove to classmates that they were not "soft" or sissyish and that they taunted boys who did well by describing them as being a "keeno".
Eastfields high boys' school in Mitcham, Surrey, was one of the worst-performing schools in last year's league tables. It fell from 18 per cent of pupils gaining five top GCSEs in 1996 to 14 per cent.
Head Stephen Harding said: "We are constantly working on specific strategies for teaching boys. Literacy is a key issue. Acquisition of language skills appears for some boys to be of a low priority and this impacts on a school's ability to deliver the curriculum effectively."
Professor Mahony said there was no quick, resource-free fix for boys' underachievement or one that everyone would agree on. She said a more co-ordinated, multi-agency approach was needed and hoped the Government's Social Exclusion Unit would focus on it.
Concern over boys' achievement is international. In Australia middle-class girls are outperforming middle-class boys at science.
Professor Mahony said the problem here was about the performance of white,working-class boys. "The gap of achievement maps socio-economic groups. "