NICE's new advice encourages far greater use of the GP physical activity questionnaire (GPPAQ) on top of the estimated nine million questionnaires that are already set to be delivered through the QOF this year.
It comes after the government opted to create a new public health domain in the QOF in the 2013/14 GP contract.
NICE's latest public health guidance advises GPs to ask patients during routine consultations whether they are getting enough exercise and offer the GPPAQ to check their activity levels, in a bid to prevent future long-term illness.
Patients who do not exercise for at least 150 minutes a week - the level recommended by the CMO - should be encouraged to do more physical exercise. Just 39% of men and 29% of women in the UK currently follow this advice, NICE said.
The institute also called on commissioners to 'raise awareness of physical activity assessment as part of relevant QOF indicators'.
This year's QOF incentivises GPs to offer annual GPPAQ checks to patients under 75 with hypertension, and offer a brief intervention to those deemed 'less than active'.
The GPC had opposed the introduction of the targets. It said nearly nine million questionnaires would need to be carried out across the UK each year, 'which would clearly have significant knock on effects to the rest of the service without any discernible benefit'.
Commenting on the new guidance, Cheshire GP Dr Matt Kearney, primary care and public health advisor to NHS England and co-author of the guidance, said 'As a practising GP, I see first-hand the effects of physical inactivity, and the lasting and serious damage it can have on people’s health.
'This guidance offers practical advice to people working in busy clinics and will help us to give straight-forward advice to people who need to improve their levels of physical activity.'
Professor Mike Kelly, director of public health at NICE, said: 'This advice sets out simple ways for family doctors, practice nurses and others working in primary care, to consider levels of physical activity in every patient they see and to help people to improve their health by boosting their activity levels. This simple advice could have a big impact on improving lives and saving taxpayers’ money.'