Professor Dame Sally Davies made the recommendation as a new guideline on healthy levels of physical activity was issued by the UK’s four CMOs.
A senior GP at the British Heart Foundation warned of the difficulties in offering such advice during 10-minute consultations.
For the first time the UK-wide guidelines advise that under-fives should have at least three hours of activity every day, once they can walk.
The report - Start Active, Stay Active - says children aged 5-18 should have at least an hour and up to several hours of activity each day. Adults ought to have a minimum of two and a half hours each week of moderate to vigorous activity.
Speaking at the launch of the report at a YMCA centre in London on Monday, Dame Sally said: ‘We’re looking for GPs to be thinking about this when they see patients. It’s about having this in mind in every consultation.’
At present, QOF indicator primary prevention 2 (PP2) awards five points for offering lifestyle advice including increasing physical activity to patients with hypertension.
GPs could also be paid to assess and offer a brief intervention to hypertensive patients deemed 'less than active' using the General Practice Physical Activity Questionnaire from next year under proposals to be considered by QOF negotiators.
But there has been no suggestion that GPs will be incentivised to offer any additional advice to other groups of patients.
Dame Sally also suggested that a brief intervention for physical activity could be added to the NHS Health Checks programme.
Cambridgeshire GP Dr Mike Knapton, associate medical director at the British Heart Foundation, supported the guidelines and said it was important for GPs to ‘redress the balance’ between simply prescribing drugs and offering general healthy lifestyle advice.
But he admitted time pressures may make it difficult for GPs to bring up the topic of physical activity during many consultations.
‘I do 35 consultations a day. It’s busy: we have quite a lot to do, especially with patients with chronic diseases,’ he said.
‘Don’t underestimate the practical difficulty of doing this in a 10-minute consultation,’ he warned.
He added: ‘If you come across as nagging, it won’t work. You’ve got to choose your moment.’
The report found just 40% of men and 28% of women in England followed previous guidelines recommending at least 30 minutes or more of moderate level activity at least five days a week.
It examined evidence showing that a sedentary lifestyle can increase the risk of cardiovascular disease, diabetes and some cancers.
Dr Knapton said offering advice on physical activity could cut the burden of these diseases.
He added that GPs should think about involving other members of the practice team in delivering such advice.