He urged the country to make concerted efforts to realise the dream of a 'Swachh' and 'Samarth' Bharat (clean and capable India).
In his message, Mr Mukherjee said, Gandhiji's ideals of non-violence, freedom, equality and religious tolerance have eternal value.
"Gandhiji taught us the value of harmonious co-existence and mutual respect. He displayed a rare constellation of abilities and showed how individuals can advance social and political change. He had an exemplary passion for justice and an indefatigable spirit of service to mankind," he said.
Mr Mukherjee said the hallmark of his personality was austerity and transparency.
On this occasion, he said, let us imbibe wisdom from Gandhiji's thoughts and actions to address the challenges that confront our nation.
"Let us ensure that Gandhiji's views on truth, morality and ethics remain integral to India's national consciousness.
Let us pay tribute to the father of our nation by keeping alive in our hearts and minds at all times the principles of tolerance and non-violence," he said.