Loss of confidence
These questions centred on "whether we can have confidence in Turkey as an ally," the official said.
"That means that some of the requests Turkey has made of us, for example in providing some of the weaponry that it would like to fight the PKK, will be harder for us to move through Congress."
The United States voiced disappointment after Turkey voted against fresh UN sanctions on Iran, which the United Nations Security Council adopted in June.
Ankara argued that Tehran should be given a chance to carry out a nuclear fuel swap deal, which was brokered by Turkey and Brazil.
Relations between Turkey and Israel were thrown into disarray after Israeli commandos on May 31 raided a Gaza-bound flotilla of six ships loaded with aid trying to run the blockade of Gaza in an operation in which nine Turkish activists were killed.
The bloodshed triggered international criticism of Israel and dealt a heavy blow to Turkish-Israeli ties.
Obama called on Turkey to cool its rhetoric about the raid when he met Erdogan at the G20 summit in Toronto in June, the FT report said.
Ayman al-Zawahiri, al-Qaeda's second-in-command, has criticised Turkey's "ties" with Israel and its role in Afghanistan, urging it to restore the traditional role of the former Ottoman Empire, in an audio message posted online.
"Change will come when the Turkish people ask their government to stop co-operating with Israel and recognising it and to stop sending their forces to kill Muslims in Afghanistan," a man identified on Sunday as Zawahiri by US monitoring group SITE said in the 20-minute audio tape.
The authenticity of the statement in which Zawahiri began by offering condolences to the families of those who were killed as well as to the Turkish people could not immediately be verified.
|Obama called on Turkey to cool its rhetoric about Israeli raid on Gaza-bound flotilla [AFP]
Last week, Turkish police detained 15 people with suspected links to the al-Qaeda network, the Anatolia news agency reported.
Turkish police regularly target suspected al-Qaeda supporters since two sets of twin suicide bombings hit Istanbul, the country's biggest city, five days apart in November 2003.
A Turkish cell of al-Qaeda was blamed for the attacks in which explosive-laden lorries first targeted two synagogues and then the British consulate and a British bank, killing 63 people, including the British consul.
Zawahiri also slammed Iran accusing it of collaborating with "crusaders" in Afghanistan and Iraq.
Al-Qaeda's number two, who has a US bounty of $25m on his head, made similar comments against the Turkish government in an Internet message late July.
At the time he also urged Turkey to assume the traditional leading role of the Ottoman Empire as the defender of Islam.