As the host state, the Malagasy government, through the CFIM as the RMIFC's hosting structure, oversees operations. A pool of informants made up of Regional Liaison Officers sent by each member state ensures permanent liaison with each state.

The Regional Liaison Officers provide maritime data at their level for the needs of the RMIFC. Liaison reports are governed by the Data Exchange and Sharing Memorandum of Understanding signed by each state at the IOC level.

The RMIFC process consists of working in collaboration with the 11 countries of the AfOA-OI region represented by the Regional Liaison Officers sent by their countries. The RMIFC reports to the Indian Ocean Commission, which was designated to coordinate the Maritime Security project in accordance with the terms of the Djibouti Declaration.