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A Palestinian official said Egypt, Qatar and the United Nations were trying to intervene to stem the violence - the worst in the Israeli-Palestinian conflict since 2019 - as the Muslim holy month of Ramadan peaks.
The Gaza health ministry said 23 Palestinians, including nine children, had been killed and 107 wounded by Israeli strikes in the destitute enclave since clashes surged on Monday.
Israel disputed the account, saying it had killed at least 15 fighters from Hamas - the dominant force in Gaza - and allied factions. It said at least six people were reported wounded by the salvoes in southern Israel.
The escalation began with confrontations at Al-Asqa Mosque in the heart of Jerusalem's walled Old City on the compound known to Jews as Temple Mount and to Muslims as the Noble Sanctuary - the most sensitive site in the Israel-Palestinian conflict.
On Monday, more than 300 Palestinians were injured there in clashes with Israeli police, who fired rubber bullets, stun grenades and tear gas in the compound, according to the Palestine Red Crescent Society. Police said 21 officers were hurt in the skirmishes.
Hamas on Monday fired on the Jerusalem area from Gaza for the first time since a 2014 war, causing no casualties but crossing what Israeli Prime Minister Benjamin Netanyahu called a "red line" which, he said, would spell fighting "that could last a while".
Hamas leader Ismail Haniyeh said it would keep fighting "as long as the Occupation (Israel) does not end all forms of aggression and terrorism in Jerusalem and Al-Asqa mosque".
The Israeli military said its air defence shot down around 90% of rockets that crossed the Gaza border. It also said the civilian toll in Gaza may have been due to Palestinian rockets falling short.
Police reported sometimes violent pro-Palestinian rallies in several Israeli Arab communities. Israel's population is 21% Arab, most of them Muslim.
In the ethnically mixed town of Lode, witnesses quoted by Israeli media said one or two armed Jews shot at rioting Arabs, killing one.
The account could not immediately be confirmed. Israeli police said it had arrested a Lode man for suspected involvement in a shooting that killed another resident and wounded two more.