The port authority for Kota Kinabalu Port is Sabah Ports SDN BHD which also manages the Sepangar Oil Terminal Port.

Kota Kinabalu Port contains about two thousand meters of berths at depths ranging from

5.5 to 10 meters. The Main Wharf 7 and Berths 1, 2, 3, 4, 5, 6, and 7 can accommodate vessels to 16 thousand DWT. With alongside depths ranging from 6.5 to 7.8 meters, the North Jetty and Berths 8 and 9 can accommodate vessels to 10 thousand DWT. Berths 10, 11, and 12 serve vessels to 6 thousand DWT and have alongside depths of from 5 to 8.5 meters.

Kota Kinabalu Port has about storage facilities covering 66 thousand square meters. Three godowns cover 18.2 thousand square meters, while the Container Freight Station covers 4.5 thousand square meters. Kota Kinabalu Port also has an open storage yard of 26.8 thousand square meters, a timber yard of 16.5 thousand square meters, and 1550 container ground slots.

The new Kota Kinabalu Port Passenger Terminal opened in 2002 and replaced the dozen scattered private jetties that had been used for passengers. Located at the old Kota Kinabalu Port Wharf, the Passenger Terminal serves boats and ferries for travelers from nearby cities and Gaya Island.

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