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Prime Minister Recep Tayyip Erdogan said at a United Nations meeting in Vienna on Wednesday, "Just as with Zionism, anti-Semitism and fascism, it has become necessary to view Islamophobia as a crime against humanity."

Mr. Kerry indirectly chastised the Turkish leader for the statement in his opening remarks following a meeting with Foreign Minister Ahmet Davutoglu, saying that it was important for all leaders to encourage a spirit of tolerance.

But Mr. Kerry was more pointed when asked about the comments during a joint news conference with Mr. Davutoglo. "We not only disagree with it. We found it objectionable," he said in response to a question.

Turkey is the fifth stop on Mr. Kerry's nine-nation tour and the first Muslim-majority nation he has visited as secretary of state.

Mr. Davutoglu, for his part, appeared unrepentant in his news conference with Mr. Kerry. The Turkish foreign minister insisted that Turkey was not hostile toward Israel and said that the downturn in relations was Israel's fault, referring to the 2010 episode in which eight Turks and an American of Turkish descent were killed when Israeli commandos boarded the lead ship of a pro-Palestinian activist flotilla that was trying to break Israel's blockade of Gaza.

"What did those nine individuals do so that with an army they were attacked as if they were aboard a hostile ship on open waters?" Mr. Davutoglu asked.

"If Israel wants to hear positive statements from Turkey it needs to reconsider its attitude both towards us and towards the West Bank," he said. A senior State Department official, who spoke under ground rules that he not be identified by name on Mr. Kerry's flight to Ankara, expressed the American position on the Turkish comments in less diplomatic terms than Mr. Kerry, saying that the pattern of Turkish denunciations of Israel was having a "corrosive effect" on American-Turkish relations.

"This was particularly offensive, frankly, to call Zionism a crime against humanity," the official said, referring to Mr. Erdogan's remarks. "It complicates our ability to do all of the things that we want to do together when we have such a profound disagreement about such an important thing."

The official said that the United States wanted to foster a thawing in relations between Turkey and Israel, but that the current ties between those two nations were "frozen."

"We want to see a normalization, not just for the sake of the two countries but for the sake of the region and, frankly, for the symbolism," the official added. "Not that long ago you had these two countries demonstrating that a majority Muslim country could have very positive and strong relations with the Jewish state."

Efforts to revive the Middle East peace process between Israel and the Palestinians and the conflict in Syria are also subjects on Mr. Kerry's agenda here.

On Thursday, Mr. Kerry promised food and medical supplies for the armed Syrian resistance fighting to depose President Bashar al-Assad and $60 million in additional assistance to the opposition coalition's political wing at a conference in Rome.

Mr. Kerry's first stop here was a ceremony at the American Embassy where he paid tribute to Mustafa Akarsu, the Turkish security guard who was killed in a Feb. 1 attack by a suicide bomber at the embassy compound. Mr. Akarsu's wife and children were in attendance as were two other Turkish guards wounded in the attack.

After his meeting with Mr. Davutoglu, Mr. Kerry headed to dinner with Mr. Erdogan. Arriving at the prime minister's residence, Mr. Kerry apologized for being a little late, noting that he had had long discussions with the Turkish foreign minister.

Mr. Erdogan said through an interpreter that the two diplomats "must have spoken about everything so there is nothing left for us to talk about."

"There's a lot to talk about," Kerry said. "We actually didn't talk about everything."