The National Child Obesity Database "significantly underestimates" the scale of the problem, a report has found.
The database, which aimed to weigh all five and 11-year olds, has been criticised by opposition politicians and health campaigners.
The information would be collated into a national database which would be the biggest of its kind in the world. The aim was to use the database to track obesity trends.
However, only 48 per cent of children participated in the survey after parents were allowed to withdraw their children, with overweight children the most likely to be withdrawn.
Liberal Democrat health spokesman Norman Lamb said: "It is unsurprising that this ill-thought-out idea hasn't worked. National monitoring where schools single out the very overweight alienates the very children it is meant to help."
David Haslam, Clinical director of the National Obesity Forum, told politics.co.uk: "The idea is brilliant, to get a database as huge as that, but it is totally flawed by the fact you can opt out of it."
But Dr Haslam said the result was "a totally useless and extremely expensive set of data with absolutely no function or meaning whatsoever".
The report on the database admits low participation has a "significant impact on data quality and seriously limit the reliability of the results for this year, as a result of which many of the figures in this report need to be treated with considerable caution".
Some 538,400 children were surveyed and 80 per cent of primary care trusts submitted the figures to the database.
However, participation varied widely and in areas with high participation, obesity rates were higher indicating low participation would lead to an under-reporting of the problem.
Conservative shadow health minister Andrew Lansley said: "Acquiring good quality data is necessary but not sufficient. It is vital to have for measuring children and young people to translate into effective programmes for increasing physical activity and improving diet."
Among the participating children, 9.2 per cent of five-year old boys and 10.7 per cent of girls were obese. The figures for the 11 year olds were higher with 18.9 per cent of boys and 15.4 per cent of girls obese.