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Egyptian President Abdel Fattah al-Sisi publicly ordered his military chief of staff on Wednesday to restore security in Sinai within three months after militants killed more than 300 worshippers, demanding "complete brutal force."

Sisi made his remarks in a televised speech to mark the birthday of the Muslim Prophet Mohammed as the country reels from the Friday massacre in a North Sinai mosque.

The Islamic State group's Egypt affiliate based in the North Sinai is believed to have carried out the attack on the mosque associated with the Sufi order.

"Allow me to take this opportunity to commit General Mohamed Farid Hegazy, in front of you and all the Egyptian people: you are responsible for restoring security and stability in Sinai within three months, you and the interior ministry," Sisi told the chief of staff in the audience.

"In three months, with God's grace, and with your help and sacrifices and those of the police, Egypt will restore stability and security in Sinai," Sisi said.

"Complete brutal force will be used. Complete brutal force."

Sisi had replaced his previous military chief of staff in October after militants ambushed policemen in the country's Western Desert, killing at least 16.

Security officials and residents said IS operatives warned elders of the village where the deadly attack took place to stop collaborating with security forces and to suspend rituals associated with Islam's Sufi movement.

Egypt's years-long campaign against an insurgency in the northern Sinai Peninsula is under increasing scrutiny following the horrifying mosque attack.

The Sinai Peninsula had long been demilitarised under the terms of the 1979 peace treaty between Egypt and Israel but as the violence intensified the government responded by ramping up its military presence, with the tacit approval of Israel.