The warplanes struck in the Sheikh Zuwaid area near the North Sinai provincial capital, al-Arish, the state-run newspaper Al-Ahram reported online, quoting witnesses.
The newspaper also reported ongoing clashes around checkpoints in al-Arish overnight after security forces fought off an initial attack on the outskirts of the city late Tuesday that injured three security personnel.
Earlier security officials said it is the first time that the army has fired missiles in Sinai since the 1973 war with Israel to recapture the Sinai Peninsula.
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Strong army and police forces were also reported to be entering mountainous areas south of al-Arish to hunt down militants.
