Child fitness is declining by 9 per cent a decade and carries a greater threat to the health of future generations than growing obesity, the Government’s chief medical officer warned today.

Sir Liam Donaldson called for a national programme of fitness testing to be piloted in secondary schools to help reverse the trend to slothfulness. Children of normal weight who are unfit face greater health risks than those who are fat but fit, he said.

Presenting his final annual report after 12 years in what has been called the toughest job in medicine, Sir Liam listed the 38 reports he has published – a work rate that far exceeded his predecessors’ – and said he was proudest of helping to bring about the smoking ban, the first legislation in the world to allow embryo research and a switch of focus in the NHS from quantity to the quality and safety of care.

His biggest regret was the Government’s failure to implement his recommendation for a minimum price on alcohol, rejected by Gordon Brown a year ago, which could have started “to turn the tide on binge-drinking”.

On exercise, his final recommendation for boosting the health of the nation, he described it as “nature’s cure” and said that if its benefits were available in pill form it would be hailed as a miracle treatment.

“Inactivity pervades the country. It affects more people in England than the combined total of those who smoke, misuse alcohol or are obese. Being physically active is crucial to good health,” he said.

Around 70 per cent of adults fail to meet the minimum recommended level of 30 minutes of physical activity five times a week, increasing their risk of six chronic diseases: heart disease, stroke, diabetes, breast cancer, colon cancer and osteoporosis.

Fitness decreases during childhood, possibly due to decreasing emphasis on physical fitness in older age groups, the report says. In California, which has had mandatory fitness testing for 10- to 15-year-olds since 2003, there was a better than 8 per cent improvement in the number of children rated fit over three years.

Sir Liam also called for a national cold weather plan to be developed, similar to the national heatwave plan, to reduce the number of excess winter deaths among the elderly. More than 30,000 extra people die on average between December and March, compared with other times of the year.

Britain’s rate is 45 per cent higher than in Finland, despite being much less cold, and is higher than many neighbouring countries, including Germany, the Netherlands, France and Italy.

“The coldest countries are very well prepared – they understand the need to keep their homes insulated and to wear more clothes when they go out better than in those countries where people are used to living in T-shirts,” he said.

Sir Liam said he expected a high toll in Britain this year because of the unusually cold weather, which causes the blood to thicken and the arteries to constrict, resulting in more heart attacks and strokes.