Only 31 per cent of 14 year-old girls exercise, compared to 50 per cent of boys of the same age.
Now schools are being urged to introduce more female-friendly fitness activities such as Zumba classes and rollerblading to encourage girls to get fit in other ways.
A study for the Women's Sports and Fitness Foundation says more than half of girls are put off by PE classes and the gap between the amount of exercise girls and boys do widens during their time at school.
The WSFF wants schools to make sports lessons more appealing to girls. The research found most girls wanted to do more physical activity, but many were put off by PE classes.
Some said they did not like exercising in front of boys, and they were not confident about their sporting skills.
A number felt teachers paid too much attention to the girls who were best at sport.
Girls were also concerned about what their friends thought about exercise, and said getting sweaty was not feminine.
Others said they did not think there were enough female sporting role models.
The WSFF is writing to schools offering advice on how to make school sports more attractive to girls.
"It's simply unacceptable that the overwhelming majority of our young women are leaving school with dangerously low levels of physical activity," said WSFF chief executive Sue Tibbals.
"We can't afford to keep ignoring the evidence that school sport plays a key role in shaping attitudes to sports and fitness."
Do you have a teenager girl who wants to exercise but is held back by confidence issues?
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