US Secretary of State John Kerry held talks with Turkey's leaders on the Syria crisis Friday amid a row over comments by the Turkish premier branding Zionism a "crime against humanity."

"Obviously we disagree with that, we find it objectionable," Kerry said at a joint press conference in Ankara, referring to a speech delivered by Prime Minister Recep Tayyip 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.

He met later Friday with Erdogan and had a "respectful but frank discussion of the prime minister's speech in Vienna," a senior State Department official said.

"The Secretary made US concerns very clear. The US and Turkish side agreed to stay in very close touch about the whole range of related issues, including their shared commitment to Middle East peace," the official said..

The top US diplomat's visit to Turkey came a day after Washington announced that it would for the first time provide direct aid to Syrian rebels in the form of food and medical supplies as well as $60 million in extra assistance to the political opposition.

But the discussions were overshadowed by renewed tension between Turkey and Israel, two major US allies, following comments Erdogan made earlier this week at a UN-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."

The incident strained bilateral military and diplomatic ties and left Washington in a bind to mend relations between its two key allies in the region.

Erdogan's comments were branded as "a dark and mendacious statement," by Israeli Prime Minister Benjamin Netanyahu while Washington said "characterisation of Zionism as a crime against humanity... is offensive and wrong."

A US official travelling with Kerry on his first trip abroad since taking over as secretary of state from Hillary Clinton said Washington was "dismayed" to hear Erdogan's remarks.

"This was particularly offensive frankly," said the official who requested anonymity.

As part of their agenda, Kerry and Davutoglu also discussed the nearly two-year civil war in neighbouring Syria which has killed at least 70,000 people according to the UN.

"Together we work to strengthen the Syrian opposition so that we are in a position now to be able to do more," Kerry said, adding that the US and Turkey were trying to reduce the money "flowing to Assad regime's war machine."

"There is no legitimacy in a regime that commits atrocity against its own people," he said.

Turkey, once a close ally of Syria, has joined the United States in its campaign to oust the regime of President Bashar al-Assad and has given shelter to Syrian rebels and to nearly 200,000 refugees along its volatile border.

In January, the US began deploying Patriot missiles, along with Germany and the Netherlands, as part of a NATO mission to protect Turkey from any spillover of the Syrian conflict.

Turkey had requested the measure after several cross-border shelling incidents, including one in October that killed five civilians.

Kerry also attended a memorial ceremony in Ankara, in honour of the US embassy guard who was killed in a February 1 suicide attack claimed by the fiercely anti-US Marxist group the Revolutionary People's Liberation Front (DHKP-C).

"The United States stands strongly with Turkey, our NATO ally, in the fight against terrorism in all its forms," including DHKP-C, al-Qaeda and the Kurdistan Workers' Party (PKK), Kerry said.

Also on the agenda during the talks was Washington's pressure for increasing sanctions on Iran over its disputed nuclear programme.