"I don't think she was treated fairly during the election, I think the coverage of her and the issues was troubling," Xinhua news agency quoted Obama as saying during his last White House press conference.
Obama expressed his grievances to the journalists who packed the White House briefing room, saying: "I'm finding it a little curious that everybody is suddenly acting surprised that this looked like it was disadvantaging Clinton."
"I do think it's worth us reflecting how it is that a presidential election of such importance, of such moment, with so many big issues at stake and such a contrast between the candidates came to 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?"
Obama's words echoed earlier remarks by Clinton who said on Thursday that Russia hacked into the Democratic National Committee and leaked emails of its officials and it was because Russian President Vladimir Putin held a personal grudge against her.
"This is not just an attack on me and my campaign, although that may have added fuel to it. This is an attack against our country," she said.
Read More: 'Putin wanted revenge on Hillary Clinton'
US media alleged that hacker groups linked to the Russian government have been actively trying to obtain information from the DNC since last year.
Obama on December 9 ordered intelligence agencies to probe the matter and reach a conclusion before he leaves office on January 20.
The effort, though enjoying bipartisan support, was slammed by President-elect Donald Trump.
"If Russia, or some other entity, was hacking, why did the White House wait so long to act? Why did they only complain after Hillary lost?" Trump tweeted on Thursday.