Two missiles were dropped near the protesters, the eyewitnesses told Anadolu Agency.
No casualties were reported so far.
Israeli army said in a statement Wednesday the raid targeted a Hamas-affiliated site in response to "fire balloons" launched on southern Israeli settlements near the Gaza strip.
Palestinian activists have been flying burning kites and balloons over Israeli territory as part of ongoing anti-occupation protests along the Gaza-Israel buffer zone.
According to Israeli officials, the improvised aerial weapons have caused a number of fires inside Israeli settlements, causing significant material damage but not resulting in any deaths or injuries.