The violence near the Gaza border comes as a Jordanian magistrate judge, Raed Zeiter who also holds Palestinian citizenship, was shot dead by IDF soldiers at a West Bank border crossing yesterday.
The IDF said Mr Zeiter tried to attack the soldiers with a metal pole, steal their weapons and then strangle them. But Palestinian witnesses claim the incident was caused by an argument over a cigarette.
Jordan's Islamic opposition movement has called on King Abdullah's government to cut all diplomatic ties with Israel in response.
In a statement issued by the Prime Minister's office, Benjamin Netanyahu said that Israel regretted the death of Judge Raed Zeiter and expressed his sympathies with the people and government of Jordan.