NTBLCP is structured along the three tiers of government i.e., Federal, State and LGA. At the federal level, the NTBLCP central unit, a division in the Department of Public Health of the Federal Ministry of Health, is responsible for policy development, resource mobilization, development of human and material resources, provision of technical support to state programmes and monitoring and evaluation of the Programme. It coordinates and collaborates with other partners to control TB, Leprosy and Buruli ulcer in the country.  The TB Technical Committee and other Technical Working Group (TWG) advises the NTBLCP to enable it to achieve its goals. 

The State TBL programmes coordinate TB, Leprosy and Buruli ulcer activities, and provide technical oversight to Programme implementation at the Local government level. The LGA is the operational level (basic management unit) of the NTBLCP. The LGAs coordinate TB, Leprosy and Buruli ulcer activities and provide technical oversight at the facility level through the Local Government TB and Leprosy Supervisor (LGTBLS). All LGA TBL supervisors should have at least one assistant to support Programme implementation at the LGA level. 

The National TB and Leprosy Training Centre (NTBLTC) is responsible for identifying the human resource needs and training various categories of healthcare staff to implement TB, Leprosy and Buruli Ulcer Control activities.