Israeli media reported that the aircraft turned out to be an Air Sinai flight from Cairo to Tel Aviv's Ben Gurion airport.
"Earlier this morning, two Israel Air Force aircraft accompanied a foreign aircraft planning to land at Ben Gurion airport which did not identify itself when entering Israeli airspace," a military spokeswoman said.
"The aircraft landed safely at Ben Gurion airport as planned," she added, without giving further details.
Last month, an EgyptAir domestic flight was hijacked and forced it to land on the Mediterranean island of Cyprus, where an Egyptian is currently in custody awaiting extradition proceedings.
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Israeli public radio said that in Saturday's incident the Air Sinai aircraft was flown by pilots new to the route and unfamiliar with the usual radio identification procedure when approaching Israel.
"The Egyptian company was asked to make the procedures clear to its pilots," the radio said.
News website Ynet, however, said that the pilot's radio silence was "apparently due to a technical fault."
Egypt and Jordan are the only Arab countries that have signed peace treaties with Israel.