Palestinians and Israeli security forces clashed in Jerusalem's flashpoint Al-Aqsa mosque compound and the surrounding Old City for a third straight day on Tuesday despite international calls for calm.

Young demonstrators gathered around the mosque threw stones at police who had entered the compound in large numbers and responded with stun grenades, an AFP journalist said.

Police said they cleared debris from the entrance of the mosque and closed the door on those inside who had been throwing stones, fireworks and other objects at security forces.

The Jordanian organisation that administers the site, the Waqf, said that police entered deep inside the mosque and caused damages.

The new flare-up came despite calls for restraint from both the United Nations and the United States. Jordan, which has custodianship rights over Muslim holy places in Jerusalem under its 1994 peace treaty with Israel, warned that relations were on the line.

The protesters fear Israel is seeking to change rules governing the site which allow Israelis to visit but not pray, although Prime Minister Benjamin Netanyahu has said the status quo will be preserved.

The site is the third-holiest in Islam but also venerated by Jews as the Temple Mount.

According to Israeli police, Palestinian youths barricaded themselves inside the mosque overnight as they had over the two previous days with the aim of disrupting visits by Jews to the compound.

Masked protesters threw stones towards the gate when regular visits to the site began on Tuesday morning, police said.

After security forces entered the compound, "masked assailants fled inside the mosque and began throwing dozens of stones" and other objects, including fireworks, police said.

There were at least four arrests, while clashes also broke out in the Old City surrounding the compound. Limited visits to the site were later allowed to go ahead.

The Palestinian Red Crescent said 26 people were wounded, of whom two were hospitalised. Israeli police said five officers were lightly injured.

Police spokeswoman Luba Samri said security forces shut the door on protesters inside the mosque in a tactic they have used in the past to restore calm.

Previous such incidents have seen police briefly enter the mosque to close the door.

"Police forces did not penetrate into the interior of Al-Aqsa mosque," Samri said in a statement.

Waqf spokesman Firas al-Dibs said "police stormed the Al-Aqsa mosque and went inside" as far as the minbar, or imam's pulpit. He said police fired rubber bullets and stun grenades that caused fires.

Clashes in the Old City appeared to be more intense than over the previous two days. Police fired stun grenades to push back protesters who threw stones and yelled: "We will never give up because Mohammed is our leader."

"The real owners of Al-Aqsa are kept outside while the thieves are inside," said a 42-year-old Arab woman, who said she came from Nazareth to protest, adding that she feared Israel was aiming to allow Jewish worship at the compound.

The three days of clashes have come as Jews celebrated their new year, or Rosh Hashanah, which began on Sunday evening and ends on Tuesday evening.

A drive by far-right Jewish groups for greater access to the mosque compound and a fringe campaign to erect a new temple have fuelled suspicions among Palestinians.

Protesters have also been angered by Israeli Defence Minister Moshe Yaalon's decision last week to outlaw two Muslim groups that confront Jewish visitors to the compound.

Israel seized 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.

Separately on Tuesday, Netanyahu will hold an "emergency meeting" of members of his cabinet involved with security to discuss ways of responding to recent incidents of stone-throwing by Palestinians in and around Jerusalem.

*This story was edited by Ahram Online