In his New Year's eve message, the President asked people to abhor violence and promote tolerance and understanding among various communities.
"I extend warm greetings and best wishes to all fellow citizens for a happy and prosperous New Year. Let 2015 be a year of peace, progress and harmony," he said.
Asking people to maintain "maximum vigilance against all efforts, from within or without, to disturb peace" and security, Mukherjee said, "let us celebrate pluralism and promote tolerance and understanding amongst all communities.
The statement comes at a time where there have been incidents of conversions by some fringe Hindu groups, blasts in Bangaluru and violence in Assam.
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In a veiled appreciation of the Modi government, he lauded a number of "new beginnings" and important initiatives launched in 2014.
"We must take these initiatives to fruition," the President said, adding, development must reach the poor and the underprivileged across the country.
He said governance, at all levels, must become efficient, transparent, accountable and citizen-friendly.
"Let us work with heart and soul and without distraction, to take our nation to new heights of achievement," he said in his message.