Formation of Cabinet Secretariat in India began with the establishment of the portfolio system. Before the advent of the portfolio system in India, the Governor-General-in-Council was accountable for all governmental dealing and the council functioned as a joint consultative board. With the increase in the burden of administrative work, the Governor-General distributed the work of different departments among various members and only important cases were referred to the Governor-General himself or the Council. The Indian Councils Act of 1861 in the time of Lord Canning formalized this procedure which led to the introduction of the portfolio system. The head of the secretariat of the executive council was the official private secretary to the Governor-General; but he did not attend the meetings of the council. It was Lord Wellington who for the first time asked his private secretary to accompany him at the meetings of the executive council and this practice was continued by his successors. But it was only in November 1935 that the private secretary was designated as Secretary to the Executive Council in addition to his other duties. A little later the two functions, namely, acting as private secretary to the Governor-General and at the same time as secretary to the council were separated and were assigned to two different persons holding two different offices.

With effect from 5th September 1946, the date of the formation of the Interim Government, an office known as the Council Secretariat came into existence. This secretariat served the Executive Council as also the coordination committee of the council set up in 1945. In 1947 a significant addition to the scope of the secretariat work took place in the form of providing secretarial assistance to the newly created defence committee of the cabinet. For providing such assistance a separate wing called the military wing was set up and its personnel were drawn from the defence services. Later this wing also took over the secretarial work of the Defence Minister`s Committee and the Chief of Staff Committee.

In 1948 the cabinet decided to start a small unit as a part of the cabinet secretariat to be known as the Economic and Statistical Coordination Unit. Its work was to secure all available information from existing statistical cells of the various ministries/departments and to present this information periodically in a proper form to the cabinet. It was also required to coordinate the activities of various ministers and to give them advice about future work. In 1949 the cabinet approved the Central Statistical Office to be attached to the secretariat and to establish a Central Statistical Unit which was set up in 1950. This unit was to function in an advisory capacity. Later in February 1951, the work relating to statistical coordination and statistical publication of a general nature, which was previously being handled by the Economic Advisor to the Government of India in the then Ministry of Commerce was transferred to the cabinet secretariat. In May 1961, a Central Statistical Organization was established and the statistical unit was amalgamated with it. This organization, thereupon, was attached to the cabinet secretariat.

The Department of Statistics was created in April 1961 as a part of the cabinet secretariat with adequate authority to consider statistical methods; to advise on and issue general directions regarding the setting up of standards, norms and methods of data collection to all central and state agencies; and to deal with references from them on such questions. With the Chinese aggression in October 1962 and the consequent declaration of a state of national emergency, the cabinet decided to set up an emergency committee to deal with the immediate issue as well as matters relating to Defence and foreign affairs. To provide secretarial assistance to the emergency committee of the cabinet and the Emergency Committee of Secretaries, and emergency wing was created in the cabinet secretariat. In July 1965 a new wing, known as the intelligence wing, was added to the secretariat to provide secretarial assistance to the Joint Intelligence Committee.

Drastic changes were made in the organization of the cabinet secretariat, consequent upon the recommendations of the Study Team on the Machinery of the Government of India and its Procedures of Work. Perhaps the most important change made, as a result of the recommendations of the Administrative Reforms Commission, was the creation of a central personnel agency in the cabinet secretariat in August 1970 and the transfer of the department of Administrative Reforms from the Home Ministry to the cabinet secretariat in February 1973. The organization of the cabinet secretariat and its role has been constantly shifting with the reorganization of the executive functions of the union government.