The ministry said two assailants on a motorcycle targeted Gen. Mohamed Said, who leads the ministry's technical office, as he left his home in Giza's Haram district, Ahram Online reported.
Egypt's interim Prime Minister Hazem el-Beblawy said Said's killing would only "fuel the authorities' determination to fight terrorism."
Condemning the incident, Beblawy said police "will keep protecting this nation no matter what."
Ahram Online said Egypt has experienced a recent surge in attacks by militants in Cairo, the Nile Delta and the Sinai Peninsula. A militant group called Ansar Bayt el-Maqdis claimed responsibility for most of the attacks.
Interior Minister Mohamed Ibrahim survived an assassination attempt in September.