(CNN) — Israeli police stormed the al-Aqsa mosque in Jerusalem's Old City early Wednesday and arrested more than 350 people, just days after a Palestinian man was killed outside the holy site.

Violent scenes inside the mosque shared on social media show Israeli forces waving flashlights and appearing to strike screaming people with batons inside the darkened building. Eyewitnesses told CNN that police smashed doors and windows, and fired stun grenades and rubber bullets.

Video shared by Israeli police shows officers entering the mosque by force with their riot shields up as fireworks are launched at them, ricocheting off the walls.

In a statement, Israeli police said its forces entered the mosque after "several law-breaking youths and masked agitators brought into the mosque fireworks, sticks, and stones."

"When the police entered, stones were thrown at them, and fireworks were fired from inside the mosque by a large group of agitators," according to the statement.

The Palestinian Red Crescent in Jerusalem said at least 12 people were injured during clashes in and around the mosque, and at least three of the injured were transferred to hospital, some with injuries from rubber bullets.

The Red Crescent added that at one point its ambulances were targeted by police and were prevented from reaching the injured.

"These instigators fortified it hours after the Taraweeh prayer in order to disrupt public order and desecrate the mosque," the police statement said. "In addition, they started chanting for incitement and violence inside the mosque and locked its doors from the inside with obstacles and fortifications at the entrances."

Police said they arrested and removed more than 350 people in the mosque, and that one Israeli police officer was wounded in the leg by stones.

Images shared on social media showed dozens of detained people lying facedown on the floor of the mosque with their legs and arms bound behind their backs, and others with their hands tied being led into a vehicle.

Overnight prayers take place in all mosques around the world especially during the Muslim holy month of Ramadan in large numbers.

The incident drew condemnation from across the Arab and Muslim world. Jordan's Ministry of Foreign Affairs condemned the actions of the Israeli police "in the strongest terms," and called on Israel to immediately remove its forces from the mosque. "The storming of the blessed Al-Aqsa Mosque and attacking it and the worshipers is a flagrant violation," said the statement, citing the ministry's official spokesperson, Sinan Al-Majali.

Jordan's Hashemite monarchy has been the custodian of Jerusalem's holy sites since 1924, and sees itself as the guarantor of the religious rights of Muslims and Christians in the city.

Egypt's Foreign Ministry also condemned the "storming" of the mosque by police, saying it had caused "numerous injuries among worshipers and devotees" and was "in violation of all international laws and customs."

The incident occurred in the middle of Ramadan, which has seen hundreds of thousands of worshipers offer prayers at al-Aqsa. Jews are set to celebrate Passover on Wednesday evening.

Over the last two weeks, there have been calls by Jewish extremist groups to slaughter goats at the compound as part of an ancient Passover holiday ritual that is no longer practiced by most Jews. A greater number of Muslim worshipers stayed in the mosque after calls came to prevent those attempts from happening.

The clashes come days after a Palestinian man was shot and killed by Israeli police at the entrance of the mosque on Saturday. Palestinian and Israeli sources disputed the circumstances that led to the killing of 26-year-old Muhammad Al-Osaibi.

In a statement Wednesday, Palestinian Authority Prime Minister Mohammad Shtayyeh condemned the actions of the Israeli police, saying: "What is happening in Jerusalem is a major crime against worshipers."

"Israel does not want to learn from history, that Al-Aqsa is for the Palestinians and for all Arabs and Muslims, and that storming it sparked a revolution against the occupation," Shtayyeh added.

The mosque compound, frequently a flashpoint in tensions, is home to one of Islam's most revered sites but also the holiest site in Judaism, known as the Temple Mount.

It has now reopened for dawn prayers, and some worshipers are being allowed to enter.

The clashes come days after a Palestinian man was shot and killed by Israeli police at the entrance of the mosque on Saturday. Palestinian and Israeli sources disputed the circumstances that led to the killing of 26-year-old Muhammad Al-Osaibi.

Gaza rockets

The Israel Defense Forces (IDF) also said on Wednesday that nine rockets were fired from Gaza Strip toward Israel.

"Following the previous report regarding the sirens which sounded in Sderot, five rockets were fired from the Gaza Strip into Israeli territory," said the IDF. "Four of them were intercepted by the aerial defense array."

The IDF also said four additional rockets launched from Gaza toward Israel but landed in open areas.

"Following the additional sirens that sounded in the surroundings of the Gaza Strip, four rockets were launched from the Gaza Strip that landed in open areas. No interceptors were launched according to protocol," the IDF added.

Ismail Haniyeh, the leader of Hamas, the militant group that runs Gaza, said in a statement "the current Israeli occupation's crimes at the Al-Aqsa mosque are unprecedented violations that will not pass."

Later on Wednesday, the Israeli military said its fighter jets had struck weapons manufacturing and storage sites in the Gaza Strip belonging to Hamas.

"This strike was carried out in response to rockets fired from the Gaza Strip toward Israeli territory earlier," it said in a statement.

Last year was the deadliest for both Palestinians in the occupied West Bank and for Israelis in nearly two decades, CNN analysis of official statistics on both sides showed.

And this year has seen a violent beginning, too. At least 90 Palestinians have been killed, according to Palestinian Ministry of Health statistics. In addition to suspected militants being targeted by Israeli forces, the dead include Palestinians killing, wounding or attempting to kill Israeli civilians, people clashing with Israeli security and bystanders, CNN records show.

In the same period, at least 15 Israelis have been killed in attacks by Palestinians in Israel and the West Bank, CNN records show — 14 civilians and a police officer who was hit by friendly fire after being stabbed by a Palestinian teenager while inspecting bus passengers.

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