Gen Ali Hersi Barre said today that a suicide car bomber detonated an explosives-laden vehicle outside a cafe near the academy.
There was no claim of responsibility for the blast, but it bore the hallmarks of the Islamic extremist group al-Shabab.
The attack comes after a US airstrike on a training camp killed more than 150 al-Shabab members on Saturday.
Despite being ousted Mogadishu and surrounding regions, al-Shabab continues to launch guerrilla attacks across the Horn of Africa country.