Israeli Prime Minister Benjamin Netanyahu vowed "war" on stone-throwers Wednesday with tougher penalties and new rules for security forces on when to open fire, following riots at a Jerusalem holy site.

Netanyahu spoke of plans to crack down on Palestinian protesters who hurl rocks and firebombs as he visited the site of a weekend car accident that killed a Jewish man.

Occupation Israeli police have said the accident was caused by Palestinian stone-throwing, the latest in a number of such incidents in and around Jerusalem.

"This stone is one too many," Netanyahu's office quoted him as saying. "We are declaring war on those who throw stones and bottles, and rioters."

Netanyahu also held an emergency meeting Tuesday with security officials and discussed minimum sentences for those who throw stones or petrol bombs, as well as his intention to alter rules of engagement.

He said authorities planned to "massively increase fines for minors and their families" involved in such activity. He has not said how rules of engagement could be altered.

The statements, while mainly referring to street protests and rioting, followed three days of clashes between Palestinians and Israeli police at Jerusalem's flashpoint Al-Aqsa mosque.

Al Aqsa mosque was calm Wednesday apart from a brief scuffle between police and members of the Waqf, the Jordanian-run organisation that administers the site.

The third-holiest site in Islam and home to the Dome of the Rock and Al-Aqsa mosque, it is also the holiest site in Judaism which venerates it as the Temple Mount.

Jews are allowed to visit but cannot pray there to avoid provoking tensions.

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

Muslim protesters 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 there.

Netanyahu has repeatedly said he is committed to the "status quo", but Palestinians remain deeply suspicious.

Palestinian president Mahmud Abbas accused Israel on Wednesday of "waging a fierce and relentless war against us in Jerusalem".

Jerusalem Mayor Nir Barkat said the latest tensions at the complex were a result of "rumours and misinformation" spread among Palestinians.

*This story was edited by Ahram Online.