Israel police spokeswoman Luba Samri said Palestinians hurled stones and glass bottles at officers after the prayers outside the site, referred to by Muslims as the Noble Sanctuary and by Jews as the Temple Mount.
The Palestinian Red Crescent said it treated at least 22 people for injuries. Police said no officers were injured; they had no information about injured protesters. The Palestinians were protesting Israel's placement of metal detectors at the entrance to the holy site after a deadly attack there last week in which three Israeli Arab gunmen killed two Israeli police officers before they were shot and killed at the entrance to the site.
Israel has defended the detectors as a necessary security measure, one it says is used routinely at holy sites around the world. But Muslim clerics have called for mass protests at the site on Friday — unless the detectors are removed by then. International efforts have been underway to try and stave off a major conflagration.
Israeli Prime Minister Benjamin Netanyahu and his security chiefs were to discuss the situation late Thursday after he returned from visits to France and Hungary. The security services are reportedly divided over what to do about the detectors, given the rising tensions surrounding the site.
Earlier in the day, Israel's public security minister, Gilad Erdan, insisted the detectors were essential to maintaining security. "The Israeli police needs these metal detectors so the security checks can give a proper response to the security considerations," he said.
Israeli security forces are on high alert ahead of Friday, when tens of thousands of Muslim worshippers typically descend on the walled compound in Jerusalem's Old City for prayers. The Palestinian militant group Hamas on Thursday called for a "day of rage" against the security measures.
Conflicts over the holy site have repeatedly triggered Israeli-Palestinian confrontations. Hamas called the initial closure of the site following last week's deadly attack a "religious war" and called on followers to attack Israelis.
Muslim clerics have been urging the faithful to skip prayers in neighborhood mosques on Friday and converge on the shrine, in an attempt to draw larger crowds. Worshippers have been asked this week to pray in the streets rather than submit to the new security procedures.
Netanyahu held urgent phone conversations with his security chiefs Wednesday and appears to be under intense international pressure to back down. Netanyahu said Israel is in close contact with Jordan, the traditional Muslim custodian of the shrine, to find a peaceful solution to the conflict. Jordan's ruling Hashemite dynasty, with ancestry said to go back to Prophet Muhammad, derives much of its legitimacy from custodianship over the shrine. The White House has also called for tensions to be reduced.
Turkish President Recep Tayyip Erdogan also called on Israel to remove the metal detectors in a phone conversation with his counterpart Reuven Rivlin. The Israeli president called last week's attack "intolerable" while officials in Erdogan's office say he told Rivlin that violence wasn't acceptable. The officials spoke on condition of anonymity in line with regulations.
Azzam Khatib, the director of the site's Muslim administration, or Waqf, said he was hopeful an arrangement could be found before the Friday prayers. "We will never ever accept any changes in the mosque, and Israel has to put an end to this crisis by removing the metal detectors," he said.
A Jerusalem resident near the site, Ruben Abu Shamsi, said he hopes "the Israeli government will be so wise to avoid the violence." Nationalist Israeli politicians have been pressuring Netanyahu from the opposite direction.
Education Minister Naftali Bennett, leader of the pro-settler Jewish Home party, warned of an Israeli "capitulation" that "will damage Israel's power of deterrence and will endanger the lives of the visitors, the worshippers and the police officers."
After last week's deadly attack, Israel closed the site for two days for searches. It was only the third closure since Israel captured the shrine, along with east Jerusalem and other territories, in the 1967 Mideast war.
The closure drew wide condemnation from the Muslim world. Israel began opening the site gradually on Sunday. Jews revere the 37-acre (15-hectare) raised platform as the site of their biblical temples. It is the holiest site in Judaism and the nearby Western Wall, a remnant of one of the temples, is the holiest place where Jews can pray.
Muslims believe the hilltop marks the spot from which the Prophet Muhammad ascended to heaven. It is Islam's third-holiest site after Mecca and Medina in Saudi Arabia. Also on Thursday, the Israeli military said it shot and killed a 26-year-old Palestinian attacker who tried to stab soldiers at a checkpoint near the West Bank city of Hebron.
In the past two years, Palestinians have killed 45 Israelis, two visiting Americans and a British tourist in stabbings, shootings and car-ramming attacks. During that same period, Israeli forces have killed more than 255 Palestinians, most of them said by Israel to be attackers while others were killed in clashes with Israeli forces.
Israel blames the violence on incitement by Palestinian political and religious leaders to commit attacks. Palestinians say the attacks stem from anger over decades of Israeli occupation of territories they claim for their future state.
Associated Press writer Mohammed Daraghmeh in Ramallah, West Bank, contributed to this report.