Before the adoption of the portfolio system in the Government of India, all Governmental business was disposed of by the Governor-General in Council, the Council functioning as a Joint Consultative Board. As the amount and complexity of business of the Government increased, the work of the various Departments was distributed amongst the members of the Council, only the more important cases being dealt with by the Governor-General or the Council collectively.

This procedure was legalized by the Indian Councils Act, 1861 during the time of Lord Canning, leading to the introduction of the portfolio system and the inception of the Executive Council of the Governor-General. The Secretariat of the Executive Council was headed by the Private Secretary to the Viceroy, but he did not attend the Council meetings. Lord Willingdon first started the practice of having his Private Secretary by his side at these meetings. Later, this practice continued and in November, 1935, the Viceroy's Private Secretary was given the additional designation of Secretary to the Executive Council. But these posts were separated subsequently, and a separate Secretary was appointed to the Executive Council as distinct from the Private Secretary to the Viceroy and Governor General.

Constitution of the Interim Government in September 1946 brought a change in the name of this Office. On 5th September, 1946, the Secretariat of the Executive Council was designated as Cabinet Secretariat, and the Secretary to the Executive Council as Cabinet Secretary. It seems, however, at least in retrospect, that Independence brought a sort of change in the functions of the Cabinet Secretariat. It no longer remained concerned with only the work of circulating papers to Ministers and Ministries, but developed into an organisation for effecting coordination between the Ministries.

The Cabinet Secretariat functions directly under the Prime Minister. The administrative head of the Secretariat is the Cabinet Secretary who is also the ex-officio Chairman of the Civil Services Board. The business allocated to Cabinet Secretariat under Government of India (Allocation of Business) Rules, 1961 includes (i) Secretarial assistance to the Cabinet and Cabinet Committees; and (ii) Rules of Business.

The Cabinet Secretariat is responsible for the administration of the Government of India (Transaction of Business) Rules, 1961 and Government of India (Allocation of Business) Rules, 1961 facilitating smooth transaction of business in Ministries/ Departments. The Secretariat assists in decision-making in Government by ensuring Inter-Ministerial coordination, ironing out differences amongst Ministries/Departments and evolving consensus through the instrumentality of the standing/adhoc Committees of Secretaries. Management of major crisis situations in the country and coordinating activities of various ministries in such a situation is also one of the functions of the Cabinet Secretariat.
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After independence, in 1949 an Economic Committee of the Cabinet was set up with its Secretariat at Ministry of Finance. In 1950 this was transferred to Cabinet Secretariat and designated as Economic Wing and ultimately merged with the Secretariat in 1955. In 1954, the Organisation and Methods Division was established under the Cabinet Secretariat which was later transferred to Ministry of Home Affairs during 1964.

In 1957, the Defence Committee of the Cabinet was constituted under Cabinet Secretariat for which officers were drawn from the Defence services. This wing was transferred during 1991 to the Ministry of Defence. Department of Statistics was created in 1961 under Cabinet Secretariat which was transferred to Ministry of Planning in Feb. 1973. Department of Special Economic Coordination was set up under Cabinet Secretariat in 1962 and later transferred to Ministry of Economic Defence Coordination and at present the Department does not exist. The Intelligence Wing was set up to provide secretarial assistance to the Joint Intelligence Committee in 1965.

The Bureau of Public Enterprises was brought under the Cabinet Secretariat for short duration from Jan. 1966 to June, 1966 and later transferred to Deptt. of Economic Affairs under Ministry of Finance and later during 1985 to the Deptt. of Public Enterprises under Ministry of Industry.
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