Around 728 settlers stormed the compound under heavy protection from the Israeli police, according to Haaretz newspaper.
Hundreds of Jewish settlers have forced their way into the Al Aqsa Mosque compound in occupied East Jerusalem as Israeli police restricted the entry of Palestinian worshippers to the site.
The police cleared Palestinians out of the sprawling esplanade outside the mosque on Sunday, while dozens of worshippers remained inside the building.
Earlier in the day, Israeli police entered the mosque compound, a sensitive Jerusalem holy site, two days after clashes with Palestinians.
The police said they were committed to facilitating freedom of worship for Jews and Muslims. But shortly afterwards, Palestinians reported brief clashes with Israeli police, just outside the mosque compound.
Palestinian medics said 10 people were wounded. Police said Palestinians had attacked buses in the occupied east Jerusalem.
A number of buses, which appeared to be carrying Jewish visitors, were damaged and police said some passengers were lightly hurt. It said they arrested two suspects and were searching for others.
Eyewitnesses said police closed the gates of Jerusalem's Old City with barriers and prevented Palestinians from outside the city from accessing the mosque.
Witnesses also said the restrictions were later eased and that police withheld the identity documents of some worshippers.
There was no comment from the Israeli police on the report.
The Palestinian Red Crescent Society said medics treated two Palestinians from injuries at the Lions' Gate, one of the gates leading to Al Aqsa Mosque.
Witnesses said one was injured by an Israeli rubber bullet and the other was assaulted by police while trying to reach the mosque for prayers.
The site is the third holiest in Islam and the holiest for Jews, who refer to it as the Temple Mount. It has long been a flashpoint for Israeli-Palestinian violence.
Since 2003, Israel has allowed settlers into the compound almost daily.
Tensions have soared in recent weeks amid a series of deadly attacks in Israel and deadly Israeli military raids across the occupied West Bank.
Israel occupied East Jerusalem, where Al Aqsa is located, during the 1967 war. It annexed the entire city in 1980 in a move never recognised by the international community.