The report said flight paths to Ben Gurion Airport had been diverted eastward, causing incoming aircraft to fly at relatively low altitudes over the Beit El area, which may have contributed to the confusion.
The military is also examining whether a police drone operating in the area at the same time may have triggered reports of unidentified aerial objects, according to the report.
The Times of Israel said there were no reports of damage to the aircraft or injuries resulting from the incident. The military did not specify what type of fire was directed at the plane.
The incident comes amid growing concern in Israel over drones launched by Hezbollah.
Israeli Prime Minister Benjamin Netanyahu has described drones as a major threat due to the difficulty of detecting and intercepting them.
Israeli officials have in recent weeks acknowledged challenges in countering explosive-laden drones launched by Hezbollah toward military positions in southern Lebanon and communities in northern Israel.
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