Just half of children have taken part in a national programme to test whether five and 11-year-olds are overweight.
Children aged five and 11 are to be tested
Some 48% of children starting and finishing primary school have been weighed in the last year - despite the original plan to weigh every child.
The figures revealed by the Association of Public Health Observatories said it was likely heavier children opted out of the tests, as they were voluntary.
Campaigners branded the exercise a "waste of time".
It was designed to gather information, not to offer overweight children support, but the government still found the outcome disappointing.
One of the main problems identified in the report published today was that children could opt out of being weighed.
It said: "The first year of data collection has been hampered by a number of practical difficulties.
"These have had 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.
"There is anecdotal evidence of higher rates of opting out of the measurement process among heavier children, which is supported by the findings of this analysis.
"This means the figures obtained from the database are likely systematically to underestimate the prevalence of overweight and obesity."
Tam Fry, board member of the National Obesity Forum, said the exercise had been a "waste of time".
The report said 538,400 children in both years were measured - about 48% of those eligible.
In all, 80% of primary care trusts returned some data on schools in their area but response rates "varied widely across England".
It warned that an analysis strongly suggested the results "significantly underestimate the prevalence of childhood obesity".
Of those children that were measured, 12.3% of girls and 13.4% of boys in the reception year were found to be overweight and 9.2% of boys and 10.7% of girls were obese.
In Year six, 13.8% of boys and girls were overweight and 15.4% of girls and 18.9% of boys were obese.
Public Health Minister Caroline Flint said the low response rate was "disappointing especially when where there has been a good response rate, the exercise has galvanised local services into action".
But she added: "We fully intend to continue with weighing and measuring for the National Childhood Database."
Norman Lamb, Liberal Democrat health spokesman, 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.
"Many will see it as a form of humiliation amongst their peers rather than a way of helping them.
"Creating a database will also be of little effect if GPs are not given the money to actually tackle the problem."
Andrew Lansley, the Shadow Health Secretary, said the government had failed to inject any urgency into efforts to tackle obesity.
"It is vital to have for measuring children and young people to translate into effective programmes for increasing physical activity and improving diet.
"This shambles over data collection is just one more public health failure by this government."