Dr Harry Burns said people had to be helped to help themselves, rather than having measures thrust upon them to reduce the health gap between rich and poor.
He said there had to be a gradual shift from a focus on treating disease to putting together projects which promote health and wellbeing.
His annual report also warned of the negative effect of the economic downturn on health.
Dr Burns said healthy life expectancy was increasing in Scotland, but there needed to be a "step change" to speed up improvements in the future.
Scotland's life expectancy is the lowest in Western Europe, and only slightly above Eastern European countries such as Slovenia and Poland.
But Dr Burns said: "What we have seen is that some of these eastern countries are catching up with Scotland."
In the Polish region of Katowice, life expectancy for women is now greater than for those in the west of Scotland - 78.6 years compared with 78.3 - whereas in the 1980s it was two years lower.
He said sociologists, psychologists and biologists had found that control was fundamental to people's health.
"Where people feel in control of their lives, when they feel that the decisions they take will be listened to, there is lots of evidence that they will be healthier. This is not just healthier in a physical sense but also mentally healthier and socially healthier.
"They will take decisions that involve them more in communities and social networks."
Dr Burns said people had to be given the skills to feel they were able to help themselves out of the situation they were in.
He highlighted the case of Bridgeton Community Learning Centre in Glasgow, which he visited yesterday, where people are given training, new skills and made to feel involved in decisions made in the areas in which they live.
Dr Burns said evidence showed people living in deprivation, with chaotic lifestyles, had higher levels of stress which in turn was linked to an increased risk of heart disease and stroke. By giving them more control and involvement in their communities, he said people would feel less hopeless and believe they could take action to improve their situation, which would lead to less stress and better health.
His annual report also warned that the economic recession could have "serious repercussions" for health among the working age population, both for those in work and those seeking employment.
With the jobless rate in Scotland rising, it highlighted the "negative impact" unemployment can have on health, arguing that those who have just lost their job should receive advice on maintaining their wellbeing while they look for work.