A church official said more families arrived in the Suez canal city of Ismailiya, a day after about 250 Copts sought shelter in one church alone there.
Three Christians have been shot dead over the past week in the city of El-Arish in the Sinai Peninsula, where Islamic State group jihadists are waging an insurgency.
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Christians have been attacked before in the Sinai, 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.
On Saturday, Sisi emphasised at a meeting with ministers "the importance of confronting all efforts to disturb security and stability in Egypt", a presidency statement said.
He ordered the authorities to help provide accommodation for the Copts fleeing Sinai, the statement added.