"We not only disagree with it, we found it objectionable," Kerry told reporters Friday in a joint news conference in Ankara with Turkish Foreign Minister Ahmet Davutoglu following a meeting to discuss the crisis in Syria, Turkey's neighbor.
Kerry said he would raise the issue directly with Ergdogan, who at a U.N. event Wednesday in Vienna, said, "As with Zionism, anti-Semitism and fascism, it is inevitable that Islamophobia be considered a crime against humanity."
Israeli Prime Minister Binyamin Netanyahu called the remark "dark and mendacious."
U.N. Secretary-General Ban Ki-moon's office said Ban heard Erdogan's speech at a U.N. Alliance of Civilizations Forum 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."
Turkish-Israeli relations have been strained since May 2010 when Israeli troops killed nine Turkish activists aboard a flotilla of aid ships trying to break through Israel's naval blockade of Gaza.
"We have never been hostile against a nation, against a state, against an individual," Davutoglu told reporters Friday. "However, if we need to speak about a very hostile practice, I would refer you to the killing of nine civilians on open waters."
Kerry was meeting Friday with Davutoglu, President Abdullah Gul and Erdogan although observers said it wasn't clear whether the meetings will help the NATO allies narrow their differences on Syria, with Turkey preferring a more aggressive approach to oust President Bashar Assad than the United States, the Hurriyet Daily News said.
A few days before Kerry's arrival in Turkey, Erdogan said, the United States "has not assumed responsibility yet. What we can discuss about and to what extent?"
Kerry announced during a "Friends of Syria" meeting in Rome Thursday the United States would commit $60 million that would be sent directly to the Syrian rebels, a first. State Department officials said the aid would be used to help local councils and communities in liberated areas in Syria, provide basic goods and services and "fulfill administrative functions including security, sanitation and education services."