The foreign ministry said in a statement that the UNESCO resolution "aims to transform the Israeli-Palestinian conflict into a religious confrontation" in an abuse of the UN agency's mandate.
"Instead of striving to reduce tensions, the authors of the resolution are working to fuel the flames in the region, using irresponsible religious rhetoric and distorting history."
UNESCO yesterday approved a highly critical resolution from a group of Arab states that condemned Israel for restricting access of Muslim worshippers to the flashpoint Al-Aqsa mosque, sacred in both Islam and Judaism.
However it did reaffirm that two other religious sites, the Tomb of the Patriarchs in Hebron and Rachel's Tomb in Bethlehem, were "an integral part of Palestine".
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The resolution comes as a wave of deadly unrest sweeps Israel and the Palestinian territories, with a series of knife, gun and car-ramming attacks as well as violent protests sparking fears of a new Palestinian intifada or uprising.
To avoid tensions with Muslim worshippers, Jews can visit the compound located in Israeli-annexed east Jerusalem but are not allowed to pray there.
However a rise in visits by Jews over their religious holidays sparked fears that Israel's right-wing government is planning to change the longstanding rule, despite Prime Minister Benjamin Netanyahu saying repeatedly he is committed to the status quo.
The resolution was drafted by Algeria, Egypt, Kuwait, Morocco, Tunisia and the United Arab Emirates, and was supported by 26 of the 58 member countries on UNESCO's board.
It also calls for the "prompt reconstruction of schools, universities, cultural heritage sites, cultural institutions, media centres and places of worship that have been destroyed or damaged by the consecutive Israeli wars on Gaza."
The Israeli foreign ministry said the decision was "another step in the continuous Palestinian endeavour to rewrite history and distort the sources of World Heritage in this part of the world.