The UNESCO executive board adopted a resolution on "Occupied Palestine" presented by several Arab countries.
The UN cultural body on Monday sought to calm anger over a resolution on a flashpoint Jerusalem holy site which saw Israel accuse it of seeking to "rewrite history".
UNESCO chief Irina Bokova called for "respect and dialogue" with regards to the Al-Aqsa mosque compound, revered by both Muslims and Jews, who refer to the site as the Temple Mount.
"Jerusalem is a Holy Land of the three monotheistic religions, a place of dialogue for all Jewish, Christian and Muslim people. Nothing should be undertaken to alter its integrity and authenticity," Bokova said in a statement.
"Only respect and dialogue can build the trust we need to move forward."
The UNESCO executive board on Thursday adopted a resolution on "Occupied Palestine" presented by several Arab countries.
The resolution outraged Israel, which it refers to several times as the "occupying power", while referring to the holy site by only its Arab name.
It criticises Israel for "excavations and works" in annexed East Jerusalem, and urges it to stop "aggressions and illegal measures against the freedom of worship and Muslims' access" to their holy site.
The resolution also accuses Israel of "planting fake Jewish graves in Muslim cemeteries."
Israeli Prime Minister Benjamin Netanyahu slammed the resolution as "yet another absurd UN decision".
"UNESCO ignores the unique historic connection of Judaism to the Temple Mount, where the two temples stood for a thousand years and to which every Jew in the world has prayed for thousands of years.
"The UN is rewriting a basic part of human history and has again proven that there is no low to which it will not stoop."
The compound in east Jerusalem, which was taken by Israel in the 1967 Six-Day War and later annexed in a move not recognised internationally, has long been a flashpoint in the conflict between Israelis and Palestinians.
Clashes have often erupted at the site in recent years, over fears that Israel is plotting to change rules which currently state that Muslims can pray there, while Jews can visit but are not allowed to pray.
Netanyahu denies seeking to allow Jews to pray at the compound.
According to biblical tradition, the first and second Jewish temples were located at the site before being destroyed by the Babylonians and the Romans.
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