Ahram Online said two gunmen riding a motorcycle opened fire on the army bus as it was traveling in al-Amireya in eastern Cairo. The attackers then fled the scene.
An army representative blamed the outlawed Muslim Brotherhood for the attack, but another security representative said militant Ansar Beit al-Maqdis was to blame, Ahram Online said.
A judiciary official said the investigation into the attack would be supervised by a military prosecutor.
Ahram Online said attacks on police and army targets have increased since the July ouster of President Mohamed Morsi, a Brotherhood follower.