Turkey's Prime Minister Recep Tayyip Erdogan has been heavily criticised by the US, Israel and the UN for branding Zionism a "crime against humanity".
He 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 strongly condemned his comments.
New US Secretary of State John Kerry said in Ankara that Washington found Mr Erdogan's remark "objectionable".
At a news conference in the Turkish capital, Mr Kerry said he had already raised the issue with Turkish Foreign Minister Ahmet Davutoglu and would also discuss it with Mr Erdogan himself.
Mr Davutoglu defended Mr Erdogan's comments.
The foreign minister again criticised Israeli troops for killing nine Turkish activists in 2010. The activists were aboard a flotilla of aid ships trying to break Israel's naval blockade of Gaza.
"If some countries acted in a hostile way against our citizens' right to life, allow us to reserve our right to make a statement," Mr Davutoglu said.
Mr Kerry is holding talks in Turkey on the escalating crisis in neighbouring Syria.
Mr Erdogan made the controversial comments at a meeting of the UN Alliance of Civilisations Forum in Vienna earlier this week.
His words drew a sharp rebuke from Mr Netanyahu's office, which called them "a dark and mendacious statement the likes of which we thought had passed from the world".
Zionism is an ideology or movement that asserts that the Jewish people have a right to a national home or state in what was the Biblical "Land of Israel".
There is no consensus among Zionists as to where the borders of the state should be.
For Palestinians, the success of Zionism has meant the frustration of their national aspirations and life under occupation.
In the US, National Security Council spokesman Tommy Vietor said "the characterisation of Zionism as a crime against humanity... is offensive and wrong".
UN Secretary General Ban Ki-moon's office said he heard Mr 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".