NTLP is under the Unit of Epidemiology and Disease Control in the Department of Preventive Services, Ministry of Health and Social Welfare. Administratively, NTLP operates at three levels: national, regional and district.

At the national level, the Tuberculosis and Leprosy Central Unit (TLCU), situated in the MOHSW, co-ordinates all activities pertaining to TB and leprosy control in the country. The Central TB Reference Laboratory (CTRL) situated at Muhimbili national hospital is part of the central unit.

TLCU is responsible for planning, monitoring, evaluation and resource mobilisation. It is also responsible for coordinating training of staff, supervision of field activities, data aggregation and analysis, quality control and operational research. On-the-job training of RTLCs and DTLCs is done during supervision visits to each region and during various meetings.