The survey of 6,500 schools, commissioned by the Department for Education and Skills, shows that only a third (37 per cent) of five and six-year-olds are doing two hours of high-quality PE and school sport a week.
In contrast, 80 per cent of 11 to 14-year-olds are meeting the target.
Overall, fewer than two-thirds of pupils (62 per cent) in school sport partnerships do so.
The survey's results were published on the same day that Professor Sir Liam Donaldson, chief medical officer, said that children need to exercise for at least an hour a day, to minimise the risk of disease later in life.
By 2006, the Government expects 75 per cent of young people to participate in two hours of high- quality physical education or school sport a week in or out of school hours.
Charles Clarke, the Education Secretary, hailed the survey as evidence of progress towards that target and said it showed the Government's pound;1 billion investment in school sport is working.
There are 8,150 schools in 222 partnerships, a third of schools in England.
Partnerships are families of schools which receive funding to improve sporting opportunities. They are typically made up of a specialist sports college, eight secondary schools and about 45 feeder primaries and special schools.
The survey shows these schools devote an average of an hour and 40 minutes per week to curriculum PE and provide pupils with the opportunity to participate in 14 different sports. A previous government survey conducted in September 2002 found that only 30 to 40 per cent of schools offered the recommended two hours.
"Exercise is essential for healthy minds and healthy bodies. School sport partnerships are bringing new opportunities to over two million pupils and are set to encompass many more schools in the next two years," Mr Clarke said.
But campaigners and opposition politicians said that the survey painted an artificially rosy picture. Schools in the partnerships are more likely to offer pupils two hours high-quality PE and sport, they said.
The Government defines high quality provision as that which is enjoyable and promotes health, well-being and continuing pupil achievement.
The survey shows schools which have been in a partnership for three years have 68 per cent of pupils taking part in two hours PE and sport each week.
The figure for schools new to the programme is 52 per cent.
Mr Clarke said the aims of the TES Get Active campaign were supported by Government policies.
A DfES guide to high-quality PE is available at www.teachernet. gov.ukpe