Para 6 of the Presidential Order dated 28th May 1990( [size:1MB] ) by which the Inter-State Council was established provides that there shall be a Secretariat comprising of such officers and staff as the Chairman may think fit to appoint. The Inter-State Council Secretariat was set up in 1991. The Secretariat is headed by a Secretary to the Government of India, assisted by two Advisers in the rank of Additional Secretary to the Government of India, two Directors and three officers each in the rank of Deputy Secretary and Under Secretary.

The secretarial functions of the Zonal Councils have been transferred to the Inter-State Council Secretariat with effect from 1st April, 2011.

The Inter-State Council Secretariat is located in Vigyan Bhawan Annexe, Maulana Azad Road, New Delhi-110 011.