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Israel called in a top Palestinian cleric from the al-Aqsa mosque for questioning on Friday, following a spike in violence in Jerusalem that saw Friday prayers at Islam's third holiest site cancelled for the first time in 17 years.

According to the cleric's son, Sheikh Mohammed Hussein was taken to an Israeli police station in Jerusalem's old city following the killing of two Israeli soldiers at the entrance to the mosque's compound.

Police say the assailants used a knife, a pistol and two homemade machine guns.

The two attackers were later killed by Israeli forces.

Israeli Prime Minister Binyamin Netanyahu said that the shutdown of the al-Aqsa mosque did not represent a change in what is called the "status quo" about custody of and access to the site.

Jordan has urged Israel to reopen the holy site.

It follows the killing of three Palestinian men and injury of two Israeli troops following a shoot out close to the Jerusalem mosque on Friday.

Violence also erupted near the West Bank town of Bethlehem.

One Palestinian man, named as 18-year-old Bara Hamamdah, was killed in the clashes, the Palestinian Health Ministry said.

Israel's military reported the fighting took place inside a refugee camp, but did not confirm Hamamda's death, saying troops were there to arrest "suspects".