The ministry said he killed two people when he opened fire on a shop before heading to the church where he shot dead seven people, including a policeman. One of the a tackers had been killed and the other captured by Egyptian security.
During a Palm Sunday service in April more than 40 people were killed and many more injured by bomb attacks in two separate cities and in May almost 30 people were killed when gunmen attacked a bus carrying Coptic Christians to a monastery.
Masked militants riding in three SUVs open fire on a bus packed with Coptic Christians, including children, south of the capital Cairo, killing at least 28 people and wounding 22 others. Isis also claimed responsibility last week for firing an anti-tank missile at a helicopter at an airport in northern Sinai as the defence and interior ministers were visiting.
He also noted that terrorist acts as such, aim at tearing the fabric of the Egyptian society which is characterized by religious unity and diversity.
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No group immediately claims responsibility for the attack, the fourth to target Christians since December of the previous year, but it bears the hallmarks of the Islamic State group's local affiliate. On Palm Sunday in April, terrorists staged an explosion in the main church of the city of Tanta, where about 30 people died.
State television reported that a second assailant who escaped had been arrested.
Security forces went on high alert for Christmas and New Year celebrations.
Egypt's Interior Ministry said one of the two attackers was killed. No suspects have been named and the case remains unresolved.