The BBC reports that at least 16 people were wounded in the unrest in Dahshur, around 40km (25 miles) south of Cairo.
The attack was triggered by the death of a Muslim man as a result of wounds sustained in clashes on Friday.
According to the Associated Press, the Coptic Archbishop of Giza reports that the town's Christian community has now fled.
Christians have experienced deadly attacks in recent years. Last October, a church in the village of Elmarinab in Edfu, Aswan province, was demolished and set alight.
In May last year, 12 people were killed and two churches set on fire during violent clashes in Cairo's Imbaba district.
That followed a New Year's Day bombing on a church in Alexandria, which killed 23 people and injured 97.