Yesterday, suspected Islamic State jihadists killed a member of the minority in the North Sinai city of El-Arish and set his house on fire.
The Coptic Church condemned the "terrorist" attacks in a statement on Facebook, saying the assaults were aimed at "dividing and torpedoing" the Egyptian people.
About 250 Christians took refuge in the Evangelical Church in the Suez Canal city of Ismailiya, said church deacon and administrator Nabil Shukrallah. "They've come running with their children. It's a very difficult situation. We're expecting 50 or 60 more," he told AFP.
Families sat in the Evangelical Church's courtyard amid bags filled with their belongings and blankets, some of them still terrified of the danger they escaped.
"We've become scared of our shadows. We're scared someone would be walking behind us and shoot us. Christians are being targeted in an ugly way," said one middle-aged man who refused to give his name.
"Some people are too scared to even open their doors to go out and buy food," he added.
Another Christian, who left Sinai with her five children, said the dangers there had put off her husband from work.
"This is not right," she said, breaking into tears.
On Wednesday, police officials said two Coptic Christians, a father and son, were shot dead behind a school in El-Arish.
Christians have been attacked before in the Sinai, where the Islamic State's Egypt affiliate is waging an insurgency, but there has been an uptick since IS released a video on Sunday calling for violence against the minority.
The video included an anti-Christian speech by a militant who later detonated an explosive vest in a Coptic church in Cairo on December 11, killing 29 people.
Copts, who make up about 10 per cent of Egypt's 90 million population, say they are sidelined in both the education system and state institutions.
Jihadists and Islamists accuse them of supporting the military overthrow of Islamist president Mohamed Morsi in 2013, which ushered in a deadly crackdown on his supporters.
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