Sir Henry Yellowlees, who has died aged 86, was chief medical officer (CMO) at the Department of Health during a decade of turbulence in the health service and political change. Within a year of his appointment in 1973 the Conservative government fell to Labour and the NHS underwent massive reorganisation as the three former separate parts were brought into a single organisation, new health authorities came into being and new appointments made in a new speciality - community medicine.

The CMO historically acts as intermediary between the medical profession and government, a task that can be fraught, for instance when government acts unilaterally to reduce pay awards recommended by the independent pay review board.

To the politician the CMO is the doctors' friend, to doctors he appears to be always responsive to his political master's voice. Since the early days of the NHS this role had never been more difficult than in Barbara Castle's two years as secretary of state for health (1974-76). She arrived determined to finish "what Nye [Bevan] had started" by removing private practice from the NHS. Overruling the advice of senior officials she pressed ahead with predictable results: the alienation of the medical profession, a 16-week working-to-contract by consultants, industrial action by medical staff and collection of 16,000 undated resignations by the British Medical Association (BMA).

This was an agonising time for a CMO, obliged to participate in all-night negotiations between an implacable secretary of state, a furious profession and equally angry ancillary staff refusing to provide essential services to those occupying private beds.

The post of CMO has always been seen within Whitehall as a heavy one, with many duties that cannot be delegated and an international role that entails a lot of travel. Sir George Godber, Yellowlees's immediate predecessor, slept on a camp bed in his office two or three nights a week. Concern about the ever-increasing workload and awareness of Yellowlees's coronary thrombosis in 1972 led Godber to propose the appointment of two chief medical officers, the senior one to take forward public health, the other the NHS. This could solve one problem - the need to have that rare individual, one with a solid background in public health but also knowledge of the health service and its management; but at lower levels within the medical civil service there were duties that crossed the divide. Yellowlees preferred to remain the sole CMO at a time that saw cuts in response to the oil crisis and a change of government in 1979.

The son of an eminent psychiatrist, Yellowlees was educated at Stowe school and University College, Oxford. Service as an RAF pilot from 1941 to 1945 delayed his entry to medical school, and he did not qualify in medicine at the Middlesex Hospital until 1950. Almost immediately he became a medical manager, acting as resident medical officer there, and his handling of an epidemic among staff brought him to the attention of Godber. After a sequence of appointments to regional hospital boards Yellowlees was seconded to the Ministry of Health in 1963, rising to become Godber's deputy in 1967 and CMO in 1973.

During his time in office, Yellowlees rationalised the role of medical advice to other government departments - the Home Office with the prison medical service, the Department of Education and the Ministry of Food and Agriculture. New medical specialities, particularly accident and emergency medicine and community medicine, came into being. In Britain legislation on lead in petrol was passed, while abroad the World Health Organisation (WHO) campaign led to the eradication of smallpox.

A long-standing concern about the long hours and uncertain career prospects of junior doctors led Yellowlees to take the first steps in reducing working hours, stimulating consultant expansion and helping the increasing number of young women doctors to stay in medicine while raising families.

Yellowlees was an outstanding administrator, totally without status consciousness, genuinely non-discriminatory and always ready to give credit where it was due. He had a strong belief in an NHS free to all and leading the field in research and innovation. He was always ready to listen to argument and adjust policy in the light of new evidence. He was keen to help the nursing and other health professionals advance their roles and status.

On leaving the Department of Health in 1983, Yellowlees worked for a year at the Ministry of Defence on a new structure for medical staff in the armed services. He then became a consultant at the WHO European office, among other tasks leading the team that successfully negotiated with Turkey and Bulgaria for the provision of healthcare for Bulgarian refugees.

He was a council member of the Medical Research Council for nine years, a General Medical Council member for 10 years and an active and vocal member of the BMA council from 1986 to 1990. He remained on the health service supervisory board for 10 years and the council of the British Nutrition Foundation for more than 20 years.

Yellowlees was a joy to work with, always considerate of staff and aware of the pressures on them, approachable, modest about his own considerable achievements, with a strong sense of humour and a charming manner. He accepted others as people who mattered, always keen to know about them and their families. He carried his responsibilities lightly but was always well aware of the possible damage to the NHS and the standing of the medical profession that could stem from ill-considered decisions made within government.

He is survived by his second wife, Mary, and the three children with his first wife, Sally.

· Henry Yellowlees, medical administrator, born April 19 1919; died March 22 2006