Almost 92,000 pupils were denied their favoured place amid competition for the best state schools, it was revealed.
Some 30,000 were rejected from at least three schools and could be forced to attend unpopular comprehensives.
The figures represent the first official breakdown of how this year's secondary school places in England were distributed.
Almost 550,000 pupils aged 10 and 11 were told last week which school they had got into for September.
Experts said that in some areas competition increased as recession-hit parents pulled children out of independent schools.
But ministers hailed the figures as evidence that Labour's controversial new rules on admissions were working.
Statistics published by the Department for Children, Schools and Families showed more pupils got their first choice school this September compared to 2008, while more children were given one of the schools on their application form.
In all, 83.2 per cent of pupils got into their preferred school compared to 82.1 per cent a year earlier.
But ministers admitted there was still "considerable variation nationally", with children significantly more likely to miss out in some areas.
This includes counties with grammar schools and many London boroughs, where parents can choose between dozens of easily accessible secondaries.
Across the capital, 34 per cent of children missed out on their favoured place.
Sarah McCarthy-Fry, the Schools Minister, said parents could fight rulings through an independent appeals system.
"Parents have the right of appeal against any application that has been turned down and over the summer, local authorities and schools will be re-allocating places where others have moved address or chosen a different education for their child," she said.
According to figures, 58 per cent of parents failed to get children into their first choice school in Slough - more than three times the national average - where competition for grammar school places is fierce.
In Buckinghamshire, which also has selective schools, almost 47 per cent of pupils missed out. Other grammar school areas mirrored the trend, with a third of children being rejected from favoured schools in Birmingham, 30 per cent in Poole, 22 per cent in Kent, on-in-five in Calderdale and 11 per cent in Lincolnshire.
Almost half of children in some areas of London also missed out.
In Wandsworth, 46.7 per cent of children failed to get into their first choice school, while figures stood at 43.5 per cent in Croydon, 42.7 per cent in Kingston upon Thames and 41.8 per cent in Merton.
The disclosure follows the introduction of Labour's new admissions code two years ago which banned schools from interviewing parents or forcing families to buy equipment from expensive suppliers amid fears children from poor homes faced discrimination. Faith schools were also required to adopt clear guidelines on the distribution of religious places.
But Annette Brooke, the Liberal Democrat children’s spokesman, said: "The only way to end this annual scramble for good school places is to raise standards in those schools which are underperforming.
“While such huge variations in school performance persist across small areas, it is inevitable that ‘good’ schools will be oversubscribed and that some pupils will lose out.
"Those parents who have not managed to get their children into any of their preferred schools are going to feel incredibly disappointed and once again we are likely to see many of them coming forward to appeal." (By Graeme Paton, Education Editor Last Updated: 2:10PM GMT 12 Mar 2009)