The ministry said the raid came on the back of intelligence that the terror cell was using several areas in southern and eastern Cairo as hideous to prepare attacks.
The operation turned into a gun battle between the alleged terrorists and security forces. Three other security forces and several elements of the terror cell were wounded in the shootout.
The Interior Ministry said cell, which embraced Takfiri ideology, was plotting attacks against Coptic Christian minority during Easter celebrations.
The Coptic, Orthodox Christians, form around 10 per cent of the Egyptian population. The group has become soft target for militants mostly in the restive Sinai province, after the ouster in 2013 of Islamist President Mohamed Morsi by incumbent leader Fattah al-Sisi.
The Coptic Easter celebration will take place on April 19.
Egypt uses the term takfiri to refer to Islamist militants who often accuse their victims of being infidels.