Delivering the second Ramnath Goenka Lecture in New Delhi, the President said the media should not take the path of least resistance, as it allows the dominant viewpoint to prevail on an issue.
He talked about the challenges and opportunities provided by social media and its impact on the traditional media.
Mr Mukherjee said the media is considered the fourth pillar of democracy, as it seeks to hold the three other pillars -- executive, legislature and judiciary -- accountable and shapes public opinion.
He said that media has the responsibility of ensuring accountability and credibility of information it puts out, and asking questions to those in power is fundamental to democracy.
"Press will be failing in its duty if it does not pose questions to powers that be," he said.
Mr Mukherjee, whose term ends in about two months, said that social media has enabled the powerless to come out of their "imposed silence" but also resulted in cacophony with so many people speaking out.
He said "good journalism" sifts and interprets the data and separates facts from what is described as "fake news".
"It ensures accuracy so that public can be better informed," he said, adding that facts must never be sacrificed.
The President said India's civilisation has always celebrated plurality.