Classroom organization is used for effective academic management and control. In the Nigerian Navy Secondary Schools, class arms are named after Fast Attack Crafts (FACs) in the Nigerian Naval Fleet in alphabetical order and a mine countermeasures vessels viz AGU, AYAM, BARAMA, DAMISA, EKPE and EKUN as well as OHUE and SIRI. Each class is controlled/coordinated by an experienced class teacher. The class teacher is assisted by two students designated as Class Captains.

The housing systems is used as the main administrative model for the affective control and management of the students. On admission, the students are allocated houses named after past chiefs of the Naval Staff and past Director of Naval Education. Presently, the schools operate four main houses. The houses are Blue, Yellow or Green, Purple and Red houses respectively.

Boarding accommodation is offered to all boarding students. Each house has a House Master attached to it. There is also a hostel Administrator of the houses. Each house has a House Captain/Prefect.