The centres at MIMA are designed to be flexible and adaptable to allow multi-disciplinary research. MIMA is organised into the following centres:

1. The Centre for Maritime Economics and Industries (MEI)
2. The Centre for Maritime Security and Diplomacy (MSD)
3. The Centre for Ocean Law and Policy (OLAP)
4. The Centre for the Straits of Malacca (SOM)
5. The Centre for Coastal and Marine Environment (CMER)

Linking all the centres is the Finance and Administration Division. This division plays a key role in supporting research at MIMA.