Two days after clashes Israeli police have entered a sensitive Jerusalem holy site and arrested at least two Palestinians.

The police cleared Palestinians out of the sprawling esplanade outside the Al-Aqsa mosque itself early on Sunday, while dozens of Palestinians remained inside the building chanting “God is greatest”.

The police said they entered to facilitate the routine visit of Jews to the holy site.

Muslim worshippers wrapped in the Palestinian flags pray during holy Islamic month of Ramadan in front of the Dome of the Rock shrine at the Al-Aqsa mosque
The site has been central to tensions in Jerusalem for many years (Mahmoud Illean/AP)

They said Palestinians had stockpiled stones and set up barriers in anticipation of violence, with the police adding they were committed to facilitating freedom of worship for Jews and Muslims.

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.

Clashes erupted at the site before dawn on Friday after police said Palestinians had hurled stones toward the Western Wall, an adjacent Jewish holy site.

Police entered in force and clashed with dozens of Palestinians shortly after dawn prayers.