Emergency services chief Mohammed Sultan said three people were also wounded in the fighting today between Morsi supporters and local residents hostile to the Muslim Brotherhood group, from which he hails.
It was not clear whether the killed were Morsi supporters or residents of Cairo's Matariya district, where the clashes took place.
Weekly demonstrations by pro-Morsi protesters have been a frequent scene, often ending violently in clashes with the security or with locals.
Their numbers on the street have sharply decreased amid a security crackdown that left hundreds killed and put at least 22,000 in jail.