Obama said Friday he had openly spoken with Erdogan about "very troubling" developments in Turkey, especially in regard to freedom of the press, religion and democracy.
"I have expressed this to him directly so it's no secret, that there are some trends within Turkey that I have been troubled with," he said during a news conference at the end of a nuclear security summit in Washington.
"There is no doubt that President Erdogan has been repeatedly elected through a democratic process, but I think the approach that they've been taking towards the press is one that could lead Turkey down a path that would be very troubling," he added.
The Turkish government is under international criticism for restricting freedom of the press and crackdown on journalists.
Activists say Erdogan has filed over 1800 court cases against critics, including many journalists, for insulting him since he took office in August 2014.
Still, Obama said that Turkey is a NATO ally and an important partner in fighting extremism.
The Turkish president was among some 50 world leaders who joined Obama at the nuclear summit to discuss ways to reduce the threat of a nuclear attack.
Erdogan's security staff clashed with angry protesters on Thursday ahead of his speech at the Brookings Institution in Washington.
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