A statement by Egyptian Security forces said that the sectarian violence was some of the worst seen in months.
Christian-Muslim confrontations have increased in Muslim-majority Egypt since the overthrow of former president Hosni Mubarak in 2011 gave freer rein to hardline Islamists repressed under his rule.
According to local reports, an angry crowd smashed shops belonging to Christians, while a Coptic day care centre and an apartment inhabited by Muslims was set on fire.
Residents said the violence broke out on Friday when a group of Christian children were drawing on a wall of a Muslim religious institute.
Muslim leaders were also quick to condemn the sectarian violence which comes as Egypt struggles with a severe economic crisis and high inflation after two years of political upheaval.
Grand Sheikh Ahmed al-Tayeb, of Egypt’s leading Islamic authority Al-Azhar, urged measures to prevent the situation from escalating and to “preserve the national character which characterises the Egyptian people, Muslims and Christians,” MENA said.
“The sectarian riots which happened in El Khusus are unacceptable and grave,” Saad al-Katatni, the head of the Muslim Brotherhood political party, said on his Facebook website. “There are some who want to set Egypt ablaze and create crises.”
President Mohamed Mursi, a Brotherhood leader elected in June, has promised to protect the rights of Copts, who make up about 10 percent of Egypt’s 84 million people.