Recep Tayyip Erdogan told a UN forum this week: “As with Zionism, anti-Semitism and fascism, it is inevitable that Islamophobia be considered a crime against humanity.”
Israeli PM Benjamin Netanyahu called the comments “dark and mendacious”.
New US Secretary of State John Kerry is expected to raise the issue when he meets Turkey’s leaders on Friday.
John Kerry is in Ankara for talks on the crisis in Syria.
But his visit has been overshadowed by Recep Tayyip Erdogan’s comments, comparing Zionism with fascism, anti-Semitism and Islamophobia, at a meeting of the UN Alliance of Civilizations Forum in Vienna earlier this week.
His words drew strong condemnation from Benjamin Netanyahu’s office, which called them “a dark and mendacious statement the likes of which we thought had passed from the world”.
In the US, National Security Council spokesman Tommy Vietor said “the characterization of Zionism as a crime against humanity… is offensive and wrong”.
UN Secretary General Ban Ki-moon’s office said he heard Recep Tayyip Erdogan’s speech through an interpreter, and called it “unfortunate that such hurtful and divisive comments were uttered at a meeting being held under the theme of responsible leadership”.
Relations between Israel and Turkey have deteriorated since May 2010 when nine Turkish activists aboard a flotilla of aid ships trying to break Israel’s naval blockade of Gaza were killed in clashes with Israeli troops.
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