"And that includes all of the public statements made by all leaders," Kerry said. He said he would raise the matter directly with Erdogan.
"I believe there is a way forward," for tolerance and the pursuit of peace, "but it obviously gets more complicated in the aftermath of a speech such as the one we heard."
Reuters news agency quoted Erdogan as telling the U.N. Alliance of Civilizations 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."
Israeli Prime Minister Benjamin Netanyahu condemned the remark Thursday, calling it a "dark and mendacious statement, the likes of which we thought had passed from the world."
Turkey is the first Muslim country Kerry has visited as secretary. His first foreign trip has been dominated by the growing crisis in Syria, which borders Turkey.
The flap was the second sour note in as many days for Kerry. On Thursday, the U.S.-backed Syrian opposition leader angrily demanded more help than Kerry had offered.
The evening meeting between Kerry and Erdogan began awkwardly, with the sometimes irascible Turkish leader noting coldly that Kerry was late. Kerry apologized, and added that he had just finished a productive meeting with Foreign Minister Ahmet Davutoglu.
"You must have spoken about everything so there is nothing left for us to talk about," Erdogan replied through a translator.
He did not smile when Kerry tried to lighten the mood.
Erdogan is a vocal Islamist, a departure from Turkey's history of firmly secular democratic rule.