All three tiers of government - Federal, State and Local - share responsibilities for providing health services and programmes in Nigeria. The Federal Government is largely responsible for providing policy guidance, planning and technical assistance, coordinating state-level implementation of the National Health Policy and establishing health management information systems. In addition, the Federal government is responsible for disease surveillance, drug regulation, vaccine management and training health professionals. The Federal Government is also responsible for the management of teaching, psychiatric and orthopaedic hospitals and also runs some medical centres.

The responsibility for management of health facilities and programmes is shared by the State Ministries of Health, State Hospital Management Boards, and the Local Government Areas (LGAs). The states operate the secondary health facilities (general hospitals) and in some cases tertiary hospitals, as well as some primary health care facilities. The training of nurses, midwives, health technicians and the provision of technical assistance to local government health programs and facilities are also the responsibility of the state authorities.

The 774 local governments oversee the operations of primary health care facilities within their geographic areas. This includes the provision of basic health services, community health hygiene and sanitation.

The inadequacy of the public health system has given increasing prominence to the private health sector, (profit and non-profit) as well as to traditional and spiritual healers.