Officers fired tear gas and stun grenades, and worshipers threw stones and other objects from the grounds of Al-Aqsa Mosque.
Palestinians reported that stun grenades were fired at the mosque compound, injuring dozens.
Firas Dibs, a spokesman for the Islamic Authority Waqf, confirmed that dozens of people were injured, while the Palestinian Red Crescent said three people were taken to hospital.
Sunday, 136 people were injured in similar clashes to the enclosure. Meanwhile, 83 other people have been hospitalized due to violence elsewhere in Jerusalem.
The complex, known to Jews as the Temple Mount and to Muslims as the Noble Sanctuary, is considered the holiest site in Judaism and the third holiest site in Islam.
It is the epicenter of conflict and has been at the center of Israeli-Palestinian violence in the past.
Tensions in the city are particularly acute as Israel celebrates “Jerusalem Day” on Monday – its annual celebration of the capture of East Jerusalem and the old walled city which is home to Muslim, Jewish and Christian holy sites, during the event. ‘a 1967 war.
Police have banned Jews from visiting the Al-Aqsa compound to mark the event in an attempt to reduce tensions.
However, police have given the green light for a traditional Jerusalem Day march in which thousands of young Jews waving the Israeli flag walk through the Damascus Gate to the Old City and the Muslim Quarter.
This year, the march coincides with the Muslim holy month of Ramadan – a time of heightened religious sensibilities.
This morning, James Cleverly, British Minister for the Middle East and North Africa, called for calm.
In a statement, he said: “The UK calls for calm and calls for an end to the violence observed in Jerusalem in recent days.
“All parties must defuse tensions in the last days of Ramadan. “
The UN Security Council has scheduled closed consultations on rising tensions. Diplomats said the meeting was requested by Tunisia, the Arab representative on the council.
Tensions have soared in recent weeks in East Jerusalem, which both Israel and the Palestinians claim.
At the start of the Muslim holy month of Ramadan, Israel blocked off a popular gathering place where Palestinians traditionally socialize at the end of their one-day fast.
The move sparked two weeks of clashes before Israel lifted restrictions.
But in recent days, clashes have resumed after Israel threatened to deport dozens of Palestinians from the Sheikh Jarrah neighborhood in East Jerusalem.