Ban's spokesman said the secretary-general had heard Erdogan's speech at a UN meeting in Vienna on Wednesday through an interpreter.
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"The secretary-general believes is it is unfortunate that such hurtful and divisive comments were uttered at a meeting being held under the theme of responsible leadership," the spokesman said in a statement.
Video courtesy of jn1.tv
Erdogan had told the UN Alliance of Civilizations meeting in Vienna: "Just as with Zionism, anti-Semitism and fascism, it has become necessary to view Islamophobia as a crime against humanity."
Ties between Israel and mostly Muslim Turkey have been frosty since 2010, when nine Turks were killed by Israeli commandos who stormed the Gaza-bound Mavi Marmara ship.
US National Security Council Spokesman Tommy Vietor said the characterization was "offensive and wrong" and said people of all religions should "denounce hateful actions and overcome ... differences."
US State Secretary John Kerry is expected to raise the issue when he meets with Erdogan and other Turkish leaders in Ankara on Friday.
Israel's prime minister accused his Turkish counterpart on Thursday of making a "dark and false" statement, while the White House also condemned the remarks.
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