The death of Raed Zueter, a Jordanian magistrate of Palestinian descent, has caused an uproar in Jordan, triggering street protests and calls in parliament to annul the 1994 peace agreement with Israel.
The IDF said that guards shot Zueter on Monday after he tried to grab a rifle from a soldier at the border crossing between the West Bank and Jordan.
Jordanian officials say Israel later apologized. Israel has shared the results of its preliminary investigation with Jordan, and agreed to a Jordanian request to establish a joint investigation into Zueter's killing.
Some of the protesters organized by Jordan's Muslim Brotherhood shoved against riot police lines Friday, trying to attack the Israeli Embassy in Amman, Jordan's capital. Police officers carrying shields and batons chased some protesters in the streets. Demonstrators also burned an Israeli flag and carried a mock coffin for Zueter.
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"We will not accept less than the annulment of the peace treaty and deportation (of) the Israeli ambassador and to announce that Jews are enemies (of) our nation," Hammam Saeed, the general secretary of the Muslim Brotherhood in Jordan, told The Associated Press. "We demand a strong reaction, not only useless talking."
About half of Jordan's population is Palestinian and public anger against Israel is common. However, Israel and Jordan, both key Middle East allies of the US, signed a peace deal in 1994 and maintain strong security ties.
US Secretary of State John Kerry has frequently consulted with Jordan's King Abdullah during the former's on-going push for a framework agreement for peace talks between Israel and the Palestinians.
Jordanian parliamentarians had posed the government with an ultimatum Wednesday demanding the expulsion of the Israeli ambassador in Amman and the recall of his Jordanian counterpart.
The ambitious ultimatum also called for the release of all Palestinian and Jordanian prisoners in Israeli jails and joint Palestinian-Jordanian control of border-crossings.
The Jordanian MPs also tried to burn an Israeli flag in the chamber, during a discussion which was wholly devoted to the Israeli role in the death of Zueter.
Roi Kais contributed to this report.