Palestinians and Israeli police clashed at Jerusalem's flashpoint Al-Aqsa mosque compound for a second straight day on Monday, prompting at least three arrests, police said.

"As the police entered the compound masked youths fled inside the mosque and threw stones at the force," a police statement said.

Police said they entered the hilltop compound to ensure that Palestinian youths massing there did not clash with Israelis during the morning visiting hours. The site is sacred to Muslims.

The statement added that three Palestinian protesters were arrested and visits by Israelis went ahead as planned to the site, the third-holiest in Islam.

An AFP journalist outside the gate saw an Israeli visitor leaving the compound scuffle with Palestinians outside.

Non-Muslims are allowed to visit the compound, but Jews must not pray or display national symbols for fear of triggering tensions with Muslim worshippers.

Muslim fear Israel will seek to change rules governing the site, with far-right Jewish groups pushing for more access and even efforts by fringe organisations to erect a new temple.

Israel occupied east Jerusalem, where Al-Aqsa is located, in the Six Day War of 1967 and later annexed it in a move never recognised by the international community.

*This story was edited by Ahram Online.