Air Transport Department is under Aviation Safety and Security Directorate (ASSRD), regulatory organ of CAAN. This department is responsible for regulation of air transport services to/ from/ within Nepal. It approves both domestic and international winder/summer flight schedules.  It issues flight permission to all domestic as well as international non-scheduled, chartered, diplomatic, experimental, rescue, survey and other emergency flights.  It carries out functions related to International Affairs and the technical information and also acts as a 'focal point' on ICAO matters making close coordination with the Director General and the Deputy Director General (DDG) of ASSRD. It formulates recommendations regarding ratification/accession of the International Instruments of civil aviation. This Department is also responsible to manage Technical Library at CAAN Head Office.

The department is comprised of one Division, one section and one unit, namely, ICAO International Affairs Division, Flight Permission Section, and Technical Information Unit (Library) respectively.