The Scottish Executive admits that the issue is under discussion as part of the national PE review which is due to be published within the next three months.
With Tony Blair set to launch a publicity campaign early in the new year to encourage Britons to exercise more in the wake of damning reports on the nation's health, secondary schools will come under increasing scrutiny.
The Government is to tackle the problem of lack of sports participation head-on in the bid for the 2012 Olympic Games to try to reverse the "couch potato" trend. Making exercise a habit from an early age will be part of the agenda with schools playing a key role.
However, there is evidence that girls - even in primary - list PE well down the list of their favourite subjects. The Youth Sport Trust in England has addressed the issue through its "Girls In Sport" campaign and the feedback shows the need for change. Reasons for girls not wishing to participate can range from the clothes they are expected to wear down to a reluctance to take part in competitive team sport.
Pilot schemes have taken place in North Lanarkshire and West Lothian to look at why girls turn their back on PE and to how they react if changes are made.
Benny Lawrie, Youth Sport Trust's national development officer in Scotland, believes that fundamental changes to the way PE is taught to girls can make a difference. "Some of it is quite basic, such as having shower curtains in changing-rooms and the type of kit girls have to wear," she says.
"It is also in the way that team sports are traditionally taught and that some girls do not like the competitive nature of sport. Girls favoured other activities such as aerobics and pop mobility and it is really a question of challenging the way PE is taught in schools and also looking at after-school sports activities."
The pilot schemes are in the early stages in Scotland and a full report is not expected until next year. More schemes will be tested in the Borders and East Ayrshire before the end of the year.
"What has been quite scary is that it seems to be happening at a younger age, even at P6-P7 level," Ms Lawrie says. "I think a lot of it has to do with confidence and self-esteem at this age as girls go through a transition period."
By working with principal PE teachers and schools sports co-ordinators, the trust hopes to have a fuller picture of the problem over the coming months.
It was set up as a charity nine years ago to look at ways of developing and implementing PE and sports programmes for children "from 18 months to 18 years".
The Girls In Sport programme has been introduced to recognise achievements by girls and a national award scheme has been set up in England.
"There are some good things happening in the new community schools in Scotland," Ms Lawrie says. "For example, in Eyemouth High, where the head of PE and school sport co-ordinator Colin Richardson have been offering alternatives for girls, with the likes of yoga and getting girls to act as lifeguards in the swimming pool instead of just taking a normal swimming session."
A study by the Health Development Agency (HDA) earlier this month found that one in 10 six-year-olds in the UK is classed as obese with the figure for 15-year-olds rising to almost one in five.
With health and fitness inextricably linked, ministers' "2020" vision is to get 70 per cent of the population physically fit by then.
"We are looking at the local level and if authorities do not have the resources to implement changes, then we can look at trying to change policy at a higher level," Ms Lawrie says.
A Scottish Executive spokesperson said: "The PE review group seeks to improve participation by pupils across the board. Low participation rates among teenage girls is something that the review group has discussed. The group's final report is expected within the next few months."