Clashes broke out Friday between Israeli police and "hundreds" of Palestinian stone-throwers at the flashpoint Al-Aqsa mosque compound in Jerusalem's Old City, police said.
"They threw stones towards the Maghrebi Gate and police went onto the plaza," police spokeswoman Luba Samri told AFP, referring to the only entrance to the compound which can be used by non-Muslims.
"There are now hundreds of people throwing stones."
Police said they had used only stun grenades against the demonstrators and that "dozens of people" had barricaded themselves inside the Al-Aqsa mosque.
Palestinian officials confirmed an unspecified number of people had barricaded themselves inside the Al-Aqsa mosque as well as the golden-topped Dome of the Rock.
"We are negotiating with the Israelis not to storm into the mosque or the Dome of the Rock and to let people out," Sheikh Azzam al-Khatib, head of the Jerusalem Waqf, told AFP.
The plaza is one of the most sensitive places in the Middle East.
It is referred to by Muslims as Haram Al-Sharif and considered the third holiest site in Islam, while it is known to Jews as the Temple Mount and is revered as Judaism's most sacred site.
Witnesses told AFP police had also fired tear gas, forcing a number of women to run for cover inside the Dome of the Rock.
"We were praying when they started shooting tear gas towards us," 58-year-old Umm Mohammad told AFP by telephone from inside the Dome of the Rock.
"At first, they were shooting at the Al-Aqsa mosque but we hid in the Dome of the Rock, and now they have started firing tear gas and sound bombs towards the gates," she said.
"Women were terrified and screaming at first, but we got over it and started shouting 'Allah Akbar' (God is greatest)," she said.
Police had no immediate number of those arrested but said several police officers had been hurt by stones and treated at the scene.
Palestinian medics said they had treated five people, some of whom were suffering from tear gas inhalation, and others who had been "beaten by the police."
Officials at the nearby Muqassed hospital said they had treated four people, including at least one who was hit by a tear gas grenade.
The clashes followed nearly a week of unrest at the flashpoint compound.
On Sunday, police used tear gas to disperse Palestinians who were throwing stones inside the compound, arresting 18 people.
On Tuesday, protesters hurled stones and shoes at police escorting Jewish and Christian visitors inside the compound, leaving one police officer slightly injured. Police arrested another two Palestinians.
And on Thursday, police arrested seven Palestinians for shouting insults at a group of Jews touring the site, fearing the confrontations would lead to further clashes.