"We are moving ahead with a comprehensive programme incorporating the latest technology, intelligence gathering and the establishment of a new police unit for dealing with incidents," Commissioner Yohanan Danino told officers.
"Jerusalem residents are entitled to a high level of personal security...And the issue is at the top of Israel Police's priorities," he said in remarks carried on the force's official Twitter feed.
No one was injured in the incident late yesterday in the flashpoint east Jerusalem neighbourhood of Silwan, where a group of Palestinians fired flares and threw petrol bombs at the building, a police statement said.
The building was one of two structures housing 10 apartments that were taken over by Jewish settlers before dawn yesterday, sparking fierce local opposition.
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Such takeovers have also been strongly condemned by the international community.
Silwan is a densely populated Palestinian neighbourhood that flanks the southern walls of Jerusalem's Old City and has been the scene of frequent clashes involving a small group of hardcore settlers, the Israeli police and stone-throwing youths.
In addition, since July's killing of a Palestinian teen by Jewish extremists and a bloody 50-day Israeli military offensive in Gaza that ended on August 26, Palestinians youths have been almost constantly on the streets throughout Israeli-annexed east Jerusalem throwing stones and petrol bombs at police, motorists and public transport.
The site is also revered by Jews as the location of the biblical Jewish temple, considered Judaism's holiest place.
Danino today vowed to restore order.
"We cannot ignore public disorder incidents; stone-throwing, attacks with fireworks, throwing of petrol bombs, which characterise riots on Temple Mount and other areas in the city and its surroundings," he said, using the Hebrew term for the Al-Aqsa compound.
The Silwan clashes erupted three weeks ago when settlers moved into more than 25 apartments in the area that they claimed to have purchased.