"Obviously we disagree with that, we find it objectionable," Kerry said at a joint press conference in Ankara with his Turkish counterpart Davutoglu.
The U.S. Secretary of State was referring to a speech delivered by Erdogan that likened Zionism to fascism and anti-Semitism.
Kerry said he would raise the issue "very directly" with Erdogan and express Washington's hopes to see the two "vital allies" work together.
The top U.S. diplomat's talks with Turkish officials were overshadowed by renewed tension between Turkey and Zionist regime, two major Washington allies, following comments Erdogan made earlier this week at a U.N.-sponsored forum in Vienna.
"As is the case for Zionism, anti-Semitism and fascism, it is inevitable that Islamophobia be considered a crime against humanity," Erdogan said on Wednesday.
Kerry said it was essential for Turkey and Israel to rekindle their "historic cooperation" but the situation got more complicated "in the aftermath of the speech that we heard in Vienna."
Turkish-Israeli relations have remained in free fall since Israeli troops raided a Gaza-bound Turkish aid ship in 2010, killing nine people.
"We have never made any hostile remarks against any nation," Turkish Foreign Minister Ahmet Davutoglu said in response to a question over Erdogan's remarks.
"If you want to talk about hostile you can call Israel's attitude that, after it killed nine civilians on high seas," he added.
"If some countries acted in a hostile way against our citizens' right to life, allow us to reserve our right to make a statement", said the Turkish foreign minister.