Officials said the aircraft was not carrying bombs, Ynetnews reported. The Palestinian Ma'an News Agency reported the unmanned aircraft's flight originated in Gaza and the aircraft flew over the city of Beersheba and several other towns.
Officials said they decided not to shoot down the drone until it was over the lightly populated area around Mount Hebron for safety reasons.
"We view this incident of attempting to enter Israeli airspace very severely and we will consider our response later," Israeli Defense Minister Ehud Barak said in a statement.
Military spokeswoman Avital Leibovi would not say whether the drone had flown over military facilities, CNN reported.