Sir Harry Burns, who is stepping down, said he was unsure whether the current system for teaching doctors before they became consultants produced the finished article needed by the NHS.
Sir Harry, 62, who has held the top medical job in the country for more than eight years and is to become professor of Global Health at Strathclyde University, also questioned the advent of "super specialists", consultants with expertise in narrow fields of medicine. He said the NHS needed more people with a broader range of skills to deliver healthcare in as flexible and efficient a way as possible.
In an interview yesterday, Sir Harry restricted any expression of frustration with the health service to the reform of medical training in recent years, a matter dealt with largely on a UK- wide basis.
The old system, under which junior doctors progressed through a series of posts as they worked towards a consultant's contract, had its faults, he said, but the current regime, under which graduation from medical school is followed by two foundation years in hospital as "run-through" training in specific specialist fields, was too compartmentalised.
He expressed concern about skills being put into compartments.
"In the old days when I was a junior doctor, if the accident and emergency department was busy, everyone went down and helped. What we are seeing now is the fact we have emergency medicine consultants and they are left to get on with it. We need to be thinking through greater resilience in the system," Sir Harry said, adding that doctors should complete more than two foundation years before specialising.
He said: "I think we have seen the emergence of super specialists and, actually, what we need are more generalists."
He is optimistic that the profession will produce a solution to the problem of a training system that is "too prescriptive".
Explaining his decision to move on, he said it would allow him to focus on the issue which has long engaged him - the difference in the levels of health and wellbeing enjoyed by the affluent and the poor.
"The focus will be on fixing things," he said, later adding that while he had been able to do a lot of work on health inequalities within the Scottish Government he had "to do a lot of other things as well, like look after the medical profession and so on".
Since he became Chief Medical Officer in 2005 the Scottish Government has created the Change Funds - pots of money which allow the NHS and other community services to work together to help prevent ill health and social problems.
He said this had sparked a number of projects which he wanted to see continue and which had attracted inter-national attention.
Asked about regular criticism from opposition politicians that not enough has been done to tackle health inequalities, Sir Harry, a father-of-six, said: "It is because they believe the way to fix health inequalities is to fix access to healthcare and the evidence is that access to healthcare is good across the whole of society. It is a basic misunderstanding."
However, he painted MSPs in a positive light, saying every health minister he had worked for wanted to do the right thing and that politicians "by and large are dedicated to the welfare of the people that they are serving".
Health Secretary Alex Neil said it had been a delight to work with Sir Harry and he had brought renewed focus to the issue of health inequalities.
Mr Neil said: "I would like to thank Sir Harry for the significant contribution he has made to health across Scotland.
"Over the past eight years, Sir Harry has provided leadership in a range of areas, from leading the response to the H1N1 swine flu pandemic in 2009, to providing health advice about Legionnaires' disease."
Welcoming Sir Harry's appointment to Strathclyde University, where he will work closely with an International Prevention Research Institute in France, the principal, Professor Sir Jim McDonald, said: "We are absolutely delighted that Sir Harry has chosen to continue his vital work in public health at Strathclyde.
"He is joining a leading international technological institution which is striving to tackle the global chall-enges surrounding health through our programmes in science, engineering, technology and policy."