Department of Fertilizers comes under the ambit of Ministry of Chemicals and Fertilizers. This Department was earlier used to be named as Department of Chemicals & Fertilizers. The genesis of the Department of Chemicals and Fertilizers can traced to the erstwhile Ministry of Production in the fifties. During that time, while "Fertilizer" subject was being dealt as a part of the Section, the subject matter of "Chemicals" was assigned to Ministry of Commerce and Industry.

The importance of the fertilizer and chemical sectors was recognized in 1963 when the subjects concerned were placed in one Department in the newly set up Ministry of Petroleum and Chemicals. In 1975, with the appointment of a separate Cabinet Minister for Chemicals & Fertilizers, the Ministry of Chemicals & Fertilizers comprising the Department of Petroleum and the Department of Chemicals & Fertilizers came into being.

A separate Ministry of Chemicals & Fertilizers came into existence in September, 1982 headed by a Cabinet Minister who is assisted by Minister of State. It was part of the Ministry of Agriculture till 1984. In June, 1991, it become part of newly created Ministry of Chemicals & Fertilizers. Department of Fertilizers came into existence as a separate Department in September, 1985 consequent upon the bifurcation of the then Ministry of Chemicals & Fertilizers. Thereafter, this Department was brought under the ambit of Ministry of Agriculture for a short duration. However, the earlier position was restored in 1992.