It is owned and managed by Philippine Ports Authority and is the baseport of the Port Management Office Zamboanga del Norte.

TMO-Dapitan's administrative jurisdiction was transferred to the Port Management Office of Ozamiz (PMO-Ozamiz) under the Port District Office of Northern Mindanao (PDO-Northern Mindanao) in 1995.

In 2009, the jurisdiction of ten government ports and two private ports were transferred to PMO-Dapitan from PMO-Ozamiz; and PMO-Dapitan was transferred back to PDO-Southern Mindanao.

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