- Board of Management: The Management of the Institute is vested with a Board of Management under the chairmanship of Joint Secretary to the Govt. of India, Ministry of Culture. The members of the Board are the Deputy Commissioner, Leh, a nominee of the Vice Chancellor of the University to which the Institute is affiliated, Director (Finance), Ministry of Culture, Govt. of India, One representative of the Ministry of External Affairs (Ex-Officio), Govt. of India, One representative of Ministry of HRD (Ex-Officio), Govt. of India, Chief Education Officer, Leh as representative of J&K Education department, One Representative of Ladakh Gonpa Association, Leh, President, Ladakh Buddhist Association, Leh, Three Buddhist Scholars nominated by Govt. of India, and CIBS Staff Representative nominated by Govt. of India. The tenure of the members of the Board of Management is for a period of three years with effect from the first meeting of the re-constitution of the Board. The Director of the Institute is the Member Secretary of the Board. The meeting of the Board of Management is convened after every six months.
- Finance Committee: As per Memorandum of Association and Rules and Regulations of the Institute, a Finance Committee is constituted under the chairmanship of Director (Finance)/ Deputy Secretary (Finance) to the Govt. of India, Ministry of Culture. Other members of the Committee consists of Deputy Secretary dealing with the affairs of CIBS, Ministry of Culture, Govt. of India, and Director of CIBS, Leh. The Administrative Officer is the member secretary of Committee. The Committee meets once or twice a year to make appropriate recommendation on the proposal involving financial implications. The Committee also reviews the Annual Accounts, Annual Budget etc. of the Institute.
- Academic Council: The Board of Management constitutes an Academic Committee consisting of eminent scholars and academicians nominated by Govt. of India to advise the Board in the Academic affairs of the Institute. The Committee meets once or twice in a year as per need to advise the Board in the respective field.
- Publication Committee: The Institute is carrying out the publication of rare books and manuscripts relevant to Buddhism, Himalayan arts, culture and languages. The proposal for the publication of the rare books is placed before the Publication Committee for review and justification for its publication before sending to the press. The Publication Committee consists of eminent scholars of the subject and experts in the field of publication.
- Research Committee: The Research Committee constituted by the Institute, conducts interview for selection of candidates for fellowships, reviews the synopsis and progress of the Research Fellows, etc.