In carrying out its operational activities, Department of Marine Transportation Engineering has formed an organizational structure that is compatible with the organizational structure of Institut Teknologi Sepuluh Nopember. In implementing the program, the Head of the Department is assisted by the Secretary of the Department, the head of the laboratory responsible for operational leadership in the laboratory and the non-academic Chief of Staff (TU Subdivision Head) who assists in Financial Resources. In conducting academic activities, the Head of Department coordinates with the head of the RMK (Cluster of Courses) in formulating and evaluating the curriculum.