The Port Department under the Government of Kerala administers the non major ports in the maritime state of Kerala before Kerala Maritime Board Act, 2017 passed by the Kerala Legislative Assembly. These Ports were administered directly by the Director of Ports. There are 17 notified non major ports in Kerala under the Port Department. Two Ports at Kovilthottam and Manakkodam got denotified.

The Department formerly Port Fund (Marine Department) under the Public Works Department administered the minor ports in the Travancore - Cochin State. With the re-organisation of the states from 1st November 1956, the minor port of Colachel of the former Travancore Cochin State was transferred to the Madras State. The minor ports in Malabar & Kasargode were transferred from Madras State to unified Kerala and were grouped together as a separate administration unit under the Additional Principal Port Officer, Kozhikode.