The executive authority of the State is vested with the Governor and it is exercised by him either directly or through the Officers subordinate to him/her, in accordance with the Constitution. The Council of Minister headed by the Chief Minister will assist and advice the Governor in exercising his powers and functions. The allocation of the business of Government among the Ministers is also made by the Governor, on the advice of Chief Minister and the transaction of the business is governed by the Rules of Business and the Government Secretariat instructions and Secretariat Office Manual.

Secretariat is the apex of the State administration and it is mainly concerned in assisting the Council of Ministers in framing of policies, approval of plans, programmes and activities for overall development of the State, the work connected with Legislation, laying down rules and procedures, financial control, general direction and monitoring and evaluating the work done by the implementing Departments/Agencies. The business of the State Government is transacted through the following Secretariat Department based on the Rules of Business.

* Agriculture
* Coastal, Shipping and Inland navigation.
* Co-operation.
* Cultural Affairs
* Election
* Environment
* Finance
* Fisheries and Ports
* Food, Civil Supplies and Consumer Affairs
* Forest and Wild Life
* General Administration
* General Education
* Health and Family Welfare
* Higher Education
* Home
* Housing
* Industries
* Information Technology
* Water Resources
* Labour and Rehabilitation
* Law
* Local Self Government
* Non-Resident Keralite