The Audit Commissionerate comprises of Headquarters and Seven Circles. In the Headquarters, presently located at Custom House, Christian Basti, Guwahati, there are four Sections namely –(1) Planning & Coordination, (2)Administration, (3)Technical, and (4) Risk Management & Quality Assurance. Each Section is headed by a Deputy/Assistant Commissioner. The seven Circles are – (1) Guwahati Circle-I, (2) Guwahati Circle-II, (3) Guwahati Circle-III, (4) Shillong Circle, (5) Dibrugarh Circle-I, (6) Dibrugarh Circle-II, and (7) Agartala Circle. Guwahti Circle-I, II & III are housed at 3rd Floor of Sethi Trust Building, Bhangagarh, Guwahati. Shillong Circle is housed at 3rd Floor of Rap's Mansion, M.G. Road, Shillong. Dibrugarh Circle-I & II are located at Dr. Lila Gogoi Path, Milan Nagar, Dibrugharh. Agartala Circle is housed at Kiran Medical Hall, Old RMS Choumohani, Agartala. Each Circle is headed by a Deputy/Assistant Commissioner and comprises of upto four Audit Groups, each having Superintendents and Inspectors.
The Commissioner is the Head of the Department supported by the Additional/Joint Commissioners in supervising the functioning of Headquarters' Sections and Circles.