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Addressing reporters at the annual end-of-the-year press conference, the president said most of the emails "contained pretty routine stuff" one would expect to find in the emails of political operatives.
But he suggested the media seized on the documents, which US intelligence agencies have said was part of a Russian cyberattack campaign, and breathed life into them.
"It just took off," Obama said. "And that concerns me and it should concern all of us."
The president also said journalists should have known that reporting on the leaks would influence the election.
"The truth is that there is nobody here who didn't have some sense of what kind of effect it might have," Obama said.
He added: "I am finding it a little curious that everybody is suddenly acting surprised that this looked like it was disadvantaging Hillary Clinton because you guys wrote about it every day. Every single week. About every little juicy little tidbit of political gospel."
Obama said he was worried that an election "of such importance" could be "dominated by a bunch of these leaks."
"What is it about our political system that made us vulnerable to these kinds of potential manipulations?" he asked.
Throughout his presidency, Obama has regularly critiqued the press.
Toward the end of the 2016 campaign, for instance, Obama raked members of the media over the coals for coverage of President-elect Donald Trump, saying he was "frustrated with how this campaign is covered."