JERUSALEM: Israeli Prime Minister Benjamin Netanyahu on Wednesday announced a toughening of the penalties for stone throwers following a third day of clashes in and around Jerusalem's flashpoint Al-Aqsa mosque compound.

Young Palestinian demonstrators threw stones at Israeli police who had entered the compound in large numbers and responded with stun grenades in fresh clashes Tuesday despite international calls for calm.

Netanyahu's announcement at the start of an emergency meeting of ministers and security officials came after the death of an Israeli driver who lost control of his car after apparently being hit by stones in Jerusalem on Sunday.

"It has been decided to toughen the measures in many areas; a modification of the rules of engagement will be examined as well as the establishment of a minimum penalty for those who throw stones," the prime minister said.

He added that there would be "significant fines" for minors who commit such offences, as well as for their parents.

"On the day before Jewish New Year, it has been proved once again that stones can kill," said Netanyahu, alluding to the death of the Israeli driver.

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

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

Jews are allowed to visit the compound at certain times, but are forbidden from praying there for fear of sparking tensions with Muslim worshippers.

The arrival of more than a thousand tourists and Jews for New Year reinforced fears among Palestinians and Muslim authorities that Israel wants to scrap the current arrangements and impose a division of the use of the compound; Jews in the morning and Muslims for the rest of the day.

During the overnight emergency meeting Netanyahu insisted that the status quo at the mosque should be maintained, under which Muslims can use it when they wish.

"Israel is determined to maintain the status quo at Temple Mount," he stressed.

Netanyahu added that he would not let the trouble-makers upset visits by Jews to the site.

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-run Waqf organisation which administers the site said police entered deep inside the mosque and caused damage.

Amman said Israel's actions amounted to "aggression" against Arab and Muslim nations, and said it was examining legal and diplomatic means to protect religious sites in the Holy City.

Jordan has custodianship rights over Muslim holy places in Jerusalem under its 1994 peace treaty with Israel.

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