Half of 11-year-olds in some parts of the country were forced to accept second, third or fourth choice schools, exposing the scale of England's admissions crisis.
An estimated 20,000 have appealed against their allocated school.
Some of the most oversubscribed schools received more than eight applications per place. One parent, Andy McGuire, said he confronted the Prime Minister on live radio after failing six times to find a secondary for his son.
Experts warned this week that the clamour for places will intensify if families are given greater freedom to choose between schools under proposals outlined in the Government's recent education white paper.
Professor Alan Smithers, from the University of Buckingham, said: "Opening up the market further will increase the number of knowing parents trying to get their children into the top schools - widening the gap between the best and worst schools."
This week backbenchers told the Government its plans to allow all schools to run their own admissions will lead to disaster. They have threatened to vote against the legislation unless concessions are made.
Yesterday Ruth Kelly, the Education Secretary, was expected to tell a conference that her plans had been deliberately misunderstood and would not mean a return to the "dark shadow" of grant-maintained schools. She said the new independent trust schools would work with others as an "integral part of their local community".
The TES surveyed almost a third of local education authorities in England and found huge disparities in the number of parents able to secure their first-choice secondary school.
It found that children living in areas with fragmented education systems, with large numbers of faith, foundation and academically selective schools, faced admissions problems.
London - where parents perhaps have the greatest choice between hundreds of easily accessible schools - is the worst-hit area.
In Barnet, north London, which has a high number of faith, foundation and grammar schools, just 52 per cent of local pupils got into their preferred school.
In Westminster, 59 per cent of parents succeeded, against 65 per cent in Croydon, 66 per cent in Sutton, 70 per cent in Brent and 72 per cent in Hillingdon and Bromley.
Disappointment was widespread despite the 33 London councils and eight areas just outside the capital co-ordinating their admissions this year.
Last month it was revealed that dozens of children, including 46 in Brent and 20 in Camden, had still not secured a place. But shortages are not limited to the capital.
The TES survey revealed that more than one in 10 children transferring from primary to secondary school in Derby, Dudley, Middlesbrough, Peterborough, Salford, Sandwell, West Midlands, and Kirklees, West Yorkshire, failed to get their first-choice school.
A government spokesman said: "The white paper will make it easier for parents to obtain a school of their choice, while improving the quality of education."