Israeli police clashed with Palestinian protesters on Tuesday in a third straight day of unrest at Jerusalem's most sensitive holy site.

Police spokeswoman Luba Samri said police entered the Al-Aqsa mosque compound early in the morning to disperse a group of protesters who had holed up inside the mosque overnight.

The protesters threw rocks, fireworks, concrete blocks and a firebomb at the officers, she said, adding that two Palestinians were arrested and five police officers were slightly injured in the violence.

A firebomb thrown at police from within the mosque ignited a rug and planks of wood stockpiled by the protesters, Samri added. Mosque officials later extinguished the fire, she said. Police released photos showing piles of charred rubble outside the mosque.

Police later managed to restore calm and open the site for visitors, Samri said, but a group of protesters remained inside the mosque.

Azzam Khatib, the director of the Waqf '€” the Islamic religious authority that oversees the compound '€” said Israeli police entered deep inside the mosque in what he called "a very dangerous development."

Police denied the allegation and said officers only removed the barricade that protesters had set up at the entrance.

The director of Al-Aqsa Mosque, Omar Kiswani, blamed Israeli police for the tensions and said the gate used for visitors to access the site should be shut. He did not comment on the protesters' alleged use of firebombs from within the sacred place, the third holiest site in Islam. Police have said that firecrackers and firebombs thrown from within the mosque have caused fires. Muslim authorities at the site have blamed damage on sparks from police sound grenades.

Nearby, more Palestinian protesters gathered and police used tear gas and stun grenades to disperse them. Later, police said a Palestinian attacked two young Jews in Jerusalem's Old City, then ran away. The attack was caught on security camera and he was later arrested, police said.

The compound in Jerusalem's Old City is a frequent flashpoint and its fate is a core issue at the heart of the Israeli-Palestinian conflict. It is known to Jews as the Temple Mount, site of the two biblical Jewish temples. Muslims revere it as the Noble Sanctuary, where they believe the Prophet Muhammad ascended to heaven.

Non-Muslim visitors are only allowed to enter the site at specific hours and are banned by police from praying there.

Muslims view these visits as a provocation and accuse Jewish extremists of plotting to take over the site. The compound often becomes the center of tensions on major Jewish holidays such as Rosh Hashana, the Jewish new year, which ends Tuesday night.

The site is so holy for Jews that they traditionally have refrained from praying on the hilltop, congregating instead at the adjacent Western Wall.

Israel's chief rabbis, as well as the rabbi of the Western Wall, have issued directives urging people not to ascend the Temple Mount, arguing that Jews could inadvertently enter the holiest area of the once-standing temple, where it was forbidden to tread.

But there is a movement advocating the rights for Jews to pray at the hilltop. Some try and get around the ban on prayers by secretly mumbling the words.

Israeli Prime Minister Benjamin Netanyahu is set to convene an emergency meeting Tuesday evening after the holiday ends to discuss ways to deal with the violence at the site, as well a recent increase in Palestinian rock throwing attacks. One such attack claimed the life of an Israeli man on Monday.

Saeb Erekat, a senior Palestinian official, blamed Israel for the unrest, claiming that Netanyahu "is trying to push us to the cycle of violence, extremism, bloodshed and chaos, taking advantage of preoccupation of the world with other issues."

Israeli Foreign Ministry spokesman Emmanuel Nahshon rejected the allegations, insisting that Israel seeks to preserve the status quo at the site. He said the recent skirmishes are "an attempt by Palestinians to change the status quo in a violent way."

Jordan, which has a peace treaty with Israel, administers Muslim religious affairs at the site and Jordanian King Abdullah II warned Israel on Monday night to restore calm.

"Any more provocations in Jerusalem, will affect the relationship between Jordan and Israel; and Jordan will have no choice, but to take action, unfortunately," he said.

The current round of tensions at the site erupted Sunday morning hours ahead of the Jewish new year holiday.

Police said clashes erupted after they entered the area to ensure security following reports that protesters were planning to disrupt visits to the area and had stockpiled firecrackers and rocks.

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