The Palestinian president has suspended all contacts with Israel until metal detectors near the al Aqsa mosque are removed.
The new security measures at the contentious holy site in Jerusalem – known as the Temple Mount by Jews and the Noble Sanctuary by Muslims – sparked violence that left three people dead on Friday.
The violence, which followed mass protests at noon prayers, saw Israeli security forces clash with Palestinians in Jerusalem and the West Bank.
The extra security measures, which also include a ban on Muslim men under 50 accessing the complex, were put in place after three Arab Israelis attacked a patrol near Lion’s Gate a week ago, killing two policemen.
The three attackers, from the city of Umm al Fahm, were all killed by Israeli security forces.
Religious clerics from the Waqf – the Jordanian trust which manages the site – had asked every mosque in the city to close and worshippers were urged to pray outside the gates of al Aqsa rather than submit to the security procedures.
Access to the compound is already difficult – or impossible – for many Palestinians.
Under the status quo – which dates back to the Ottoman period – only Muslims have the right to worship on the plaza, although Jews and people from other faiths can visit.
Different residency rights have been introduced by Israel since it captured the West Bank, Gaza and East Jerusalem in the 1967 Six-Day War.
Since Israel captured the Old City it has remained committed to that formula.
However, Palestinians claim the extra security measures represent a change and a further erosion of their rights to access to the holy site.