Mohammed Hussein, the Palestinian mufti, and Raed Salah, the head of Israel's Islamic Movement, have urged people to mobilise against continuing Israeli excavations that Muslims say endanger the al-Aqsa mosque compound site.
Only Muslim men aged over 50 and in possession of Israeli identity cards are being allowed to attend Friday prayers at the mosque, although there are no restrictions on women. Communal Friday prayers are a religious obligation for Muslim men.
Al Jazeera's Barnaby Philips said men who had been prevented from entering the mosque were praying outside on the street and that at least three people had been arrested.
Illegal demonstration
A Jerusalem court has banned Salah from coming within 150m of the Old City walls for two months, after finding him guilty of participating in an illegal demonstration against the work and assaulting a police officer.
Salah vowed to ignore the Israeli court's order.
"I have the right to enter al-Aqsa," Salah told Al Jazeera. "We have the right to protect the al-Aqsa mosque and confront the Israeli occupation.
"I hope that 10,000 of our people will head towards al-Aqsa mosque today [Friday]."
Israel's increased police presence comes after 15 police and at least 20 Palestinians were wounded in clashes at the al-Aqsa compound on a similar day of protest against the Israeli works last Friday.