Palestinian medics said that 88 people had been taken to hospital and more than 200 injured, mostly by rubber bullets, stun grenades and beatings, amid protests over threats of eviction and perceived attempts to curb religious freedom among Muslims in Jerusalem.
Police said one officer was injured during the protests after being struck with a rock.
On Saturday evening, a crowd of Palestinian protesters gathered outside the Old City’s Damascus Gate, chanting “God is great”. Some threw rocks and water bottles at police as well as lighting fires and tearing down police barricades.
Police mounted on horses fired stun grenades into the crowd, while water cannons were discharged from police trucks.
At the nearby Al-Aqsa mosque, one of the holiest sites in Islam, some 90,000 people were gathered for nighttime prayers, according to Islamic authorities, to mark Laylat al-Qadr, or Night of Destiny, the most sacred night in the holy month of Ramadan.
Police reported that clashes had broken out near the mosque earlier on Saturday in the East Jerusalem neighbourhood of Sheikh Jarrah. Dozens of Palestinians fought Israeli settlers' attempts to evict them from their homes. Several arrests were made, and one officer was struck in the face by a rock, police said.
Prime minister Benjamin Netanyahu said that he “firmly rejects” pressure not to build in Jerusalem.
“To my regret, this pressure has been increasing of late,” he said during a televised address.
“Jerusalem is Israel’s capital and just as every nation builds in its capital and builds up its capital, we also have the right to build in Jerusalem and to build up Jerusalem. That is what we have done and that is what we will continue to do.”
Mr Netanyahu considers the entirety of Jerusalem to be Israel’s capital, a status not recognised abroad.
Earlier on Saturday, police angered Arab citizens by stopping a convoy of buses heading towards Jerusalem for Ramadan prayers. The travellers were upset that they had been stopped without explanation on a hot day during which they were fasting, and blocked the road in protest. It was reopened several hours later.
Israel’s public broadcaster Kan said police stopped the buses for a security check, while Ibtasam Maraana, an Arab member of parliament, accused them of a “terrible attack” on religious freedom. She tweeted: “Police: Remember that they are citizens, not enemies.”
The Israeli police force defended its actions as a security operation.
Pope Francis has called for an end to the unrest in Jerusalem and invited parties to find a solution that respects the city's multicultural identity.
“Violence breeds violence, stop clashes,” he told people gathered in St Peter’s Square on Sunday.
But the region is braced for more clashes in coming days. Early on Sunday, the Israeli military said that they had carried out an airstrike on a military post for Hamas in Gaza after Palestinian militants fired a rocket at the country’s south. No casualties were reported.
The current wave of clashes broke out three weeks ago at the beginning of Ramadan, when Israel restricted gatherings outside the Old City. They were later lifted, but anger reignited as Palestinians were threatened with eviction in East Jerusalem.
On Friday, more than 200 Palestinians and 18 officers were injured during a night of unrest at the Al-Aqsa mosque. The violence was condemned by the United States, the United Nations, the European Union and Russia, as well as by Egypt, Jordan, Bahrain and the United Arab Emirates.
In response, the Arab League scheduled an emergency meeting on Monday morning. Also expected on Monday is a court verdict on the planned evictions in Sheikh Jarrah.
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