Rates of obesity are increasing
A University of Bath study of 5,595 children found that 95% of boys and 99.6% of girls fell short of this time.
The Archives of Disease in Childhood study follows a warning that the NHS must do more to counter obesity.
The report paints a bleaker picture than the last Health Survey of England, in 2002, which claimed that many more children were meeting the standard.
The study centred on a group of children from the greater Bristol area monitored since birth by scientists seeking to unravel links between lifestyle and illness.
In this study, 5,595 boys and girls were fitted with an "accelerometer" - which measures precisely how they move, and can detect moderate or strenuous exercise - for seven days.
It revealed that children averaged just 17 minutes of moderate exercise, and two minutes of "vigorous" exercise a day.
Calum Mattocks, one of the researchers, said they were "surprised" to find so few children managing an hour of physical activity over the course of a day.
He said that even though the hour target was the result of expert consensus, it was possible that it was too ambitious.
"This suggests it's asking a lot to expect children to do an hour of moderate or vigorous exercise a day."
He added: "We should remember that, even though it does not appear that children are doing much exercise, they are still doing, on average, twice as much as adults."
The research paints a far bleaker picture of children's exercise rates compared with the official figures within the Health Survey for England.
The most recent survey, in 2002, suggested that 77% of boys and 64% of girls were meeting the standard at the age of 11.
Too little exercise in childhood has been linked to an increased risk of obesity in adulthood, which in turn raises the risk of serious diseases such as heart disease or cancer.
This week, a report commissioned by the King's Fund suggested that the rising rate of obesity, and the associated extra costs of healthcare for those affected, posed a greater risk to the future of the NHS than had been previously suggested.
British Heart Foundation
Sir Derek Wanless, who wrote the report, said: "Nobody knows how big the bills are going to be but they look quite frightening."
Dr Richard Winsley, from the Children's Health and Exercise Research Centre at Exeter University, said that evidence from other studies suggested that even more than an hour's exercise might be needed by children to protect their future health.
He said: "When you think about playtime, getting to and from school, running around at home, it's quite possible to have an hour's exercise at this age.
"Young children love to run around, and if you give them a safe place to do it, they will do it."
Steve Shaffelberg, of the British Heart Foundation, said: "We are all becoming expert at engineering physical activity out of our daily lives.
"In the last 20 years school car journeys have more than doubled, with less than 50% walking and just 1% cycling.
"The killer combination of far too little physical activity together blended with a diet heavy with soft drinks and snacks is driving rising rates of obesity among British children, and threatening their health."
A government spokesman said tackling obesity was a top priority, and a new strategy would be published in the autumn.
He said: "There are no overnight, easy solutions to creating a culture where every child has a healthy life, actively supported by their parents.
"We absolutely recognise that we must go further and faster."