The Secretariat system of administration in Puducherry is a post merger innovation. Under this system, the Secretariat Departments deal with all policy matters. All dealings and correspondence with the Central Government and other State Governments are also attended to by the Secretariat Departments.

With effect from 1st July 1963, the business of the Government came to be transacted in 12 Departments as enumerated in the schedule to the Business of the Government of Puducherry (Allocation) Rules, 1963. Thereafter, based on the acceptance of the recommendations on Restructuring the Secretariat Departments by the Government of Puducherry and the approval conveyed by the Ministry of Home Affairs, Government of India for amendment of the Business of the Government of Puducherry (Allocation) Rules, 1963 vide letter No.U-11022/2/85-UTL dated 12th March 1985, the Business of the Government of Puducherry (Allocation) Amendment Rules 1985 were subsequently notified vide G.O.Ms.No.49 dated 16th April 1985 of the Confidential and Cabinet Department, Puducherry. In the Schedule to the Rules ibid, 14 Departments have been enumerated. Confidential and Cabinet Department, General Administration Department and the Department of Personnel and Administrative Reforms are a few among them.