"I am saddened that these kinds of comments have been made in my absence," Erdogan told Turkish reporters in Washington as he rounded off a trip to the United States.
"These issues did not come onto the agenda in our talks with Mr Obama."
"He did not talk to me about this kind of thing. In our previous telephone conversations we talked about other more useful things than press freedom," the Hurriyet daily and other newspapers quoted him as saying.
Obama -- who met Erdogan in Washington for closed door talks on Thursday -- said on Friday it was "no secret" he was troubled by "some trends" within Turkey.
"I think the approach they have been taking toward the press is one that could lead Turkey down a path that would be very troubling," said Obama.
The US leader said he had expressed these sentiments to Erdogan "directly".
Erdogan said he had pointed out in other meetings on his trip in Washington that there was press freedom in Turkey, saying that Turkish publications were calling him things like "thief" and "killer" without being shut down.
"Those publications that make these insults still exist," he said. "If it was true that Turkey was a dictatorship, then how could such publications come out?" he asked.
"Such insults and threats are not permitted in the West."
"Had Obama put these issues (about press freedom) on the agenda in the talks, then I would have told him that," he added.
There has been growing concern about press freedoms in Turkey under Erdogan, with thousands of people prosecuted for insulting the president and two top journalists from the opposition Cumhuriyet daily on trial for revealing state secrets.
Before the meeting with Obama, there were also ugly scenes when Erdogan gave a speech at the Brookings Institution, a Washington think tank, with Turkish security officials clashing with protesters.