He also underscored the need for greater accomodation in public discourse as democracy will be the "loser" if people refused to hear voices other than their own.
Delivering the Ramnath Goenka Memorial Lecture, he said all stakeholders in a democratic system, from parties to business leaders, citizens to institutions, have to realise that asking questions is good and healthy.
Mukherjee said people in power, across the spectrum of politics, business or civil society, by virtue of the position they enjoy, tend to dominate the discourse and influence its direction.
"Thus the need to ask questions of those in power is fundamental for the preservation of our nation and a truly democratic society," the president said.
He said this role of asking questions has been traditionally played by the media.
"It (media) must raise and create awareness about issues concerning public welfare, hold public or private institutions and their representatives accountable for their actions or indeed, their inaction.
"In particular, the media has a duty to give space to the millions who still face the injustices of deprivation, gender discrimination, caste and social bias," Mukherjee said.
"The question that faces all of us including the media is whether we will choose to define ourselves as a nation enriched by the diversity of views or allow partisan views to dominate our national narrative?
"We ought to remember that democracy will be the loser when and if we cease to hear voices other than our own," the president said.
Mukherjee also raised concern over the danger of paid news and asked news organisations to restore objectivity to regain public trust.
"They also reduce the plurality and diversity of the media. Objectivity has to be restored to regain public trust," he said.
Mukherjee said media houses needed to ask themselves how they can find sustainable economic models that will allow them to resist all kinds of pressures and let them perform their role with honesty and transparency.
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