NTEP structure comprises of State, district, sub-district and peripheral health institution level. The States have total ownership and accountability for the TB control in the state.

The State TB Cell(STC) is the state-level implementing structure of the National TB Elimination Program (NTEP). It is the leading institution for management of NTEP activities at the state level. The STC is a State Government entity that acts as a bridge between the Central and State Governments for implementing the program. It works under the guidance of the Central TB Division (CTD) and oversees the program implementation at the districts.

A full-time State Tuberculosis Officer (STO), trained at national level and based at the State TB Cell (STC), is responsible for planning, training, supervising and monitoring the programme in all the districts of their respective states. STO is administratively accountable to the State Government, technically follows the instructions of the CTD, and coordinates with CTD and the districts and is assisted by other technical & secretarial staff.
State TB cell is being supported by State TB Training and Demonstration Centre (STDC) in many states through its three units – a training unit, Supervision and monitoring unit and an Intermediate Reference Laboratory (IRL) supporting an effective Quality Assurance system of the Sputum smear microscopy network and laboratory services for PMDT (molecular DR testing and C&DST) in the State. Operational Research is also a component of STDC. Each state also has one fully operational State Drug Store (SDS) for each 5 crore of population. It is responsible for effective management of medicines and other logistics and ensuring uninterrupted supply of good quality 1st & 2nd line anti-TB medicines for adults and paediatric population.