The Health and Family Welfare (H&FW) Department is organized into a number of directorates whose work is monitored and coordinated by the H&FW Department at the Secretariat. The department functions under the overall guidance of the Minister-in-charge, Dr. Surya Kanta Misra. The H&FW Department is headed by the Health Secretary who also oversees the working of various directorates and develops various policies which gets implemented after the approval of the Minister-in-charge.

The State Health Administration has two arms, the Secretariat and the Directorate of Health. The Secretariat is headed by the Principal Secretary who is a senior officer of the Indian Administrative Service assisted by Special, Joint, Deputy and Assistant Secretaries. The Director of Health Services and ex-officio Secretary heads the Directorate and is the chief technical Advisor to the State government on all matters related to medical and public health. He is assisted by a number of Additional, Joint, Deputy and Assistant Directors.

The heath care system has primary health care network, a secondary care system comprising district and sub-division hospitals and tertiary hospitals providing specialty and super specialty care. Each of the seventeen districts is headed by a Chief Medical Officer of Health (C.M.O.H.), assisted by Deputy and Assistant C.M.O.H.s, whose responsibility is to manage the primary health care sector and ensure the effective implementation of the various medical, health and family welfare programmes. The secondary level hospitals are headed by medically trained superintendents who report to the C.M.O.H. and are accountable to a hospital management committee. At the block level, the Block medical officer is responsible for providing services and for monitoring and supervising the primary health centres and health programme implementation.

The medical manpower in the State Health System is provided by the State Health Service and in the teaching institutions by the Medical Education Service. The training activities are mainly organised at the Institute of Health & Family Welfare, Salt Lake, Kolkata, and also at various training schools.