"Nation remembers former Prime Minister Smt Indira Gandhi on her birth centenary," President Kovind tweeted.
PM Modi tweeted" "Tributes to former PM Mrs. Indira Gandhi on her birth anniversary."
Senior Congress leaders, including former Prime Minister Manmohan Singh, party chief Sonia Gandhi and vice president Rahul Gandhi, also paid homage to the late leader.
"No one can erase Indiraji's memory," Mr Mukherjee said at an event later at 1 Safdarjung Road, where Indira Gandhi was assassinated by her bodyguards on October 31, 1984. A photo exhibition has been organised there to mark her 100th birth anniversary.
Sonia Gandhi said Indira Gandhi took pride in India's rich diversity and its democratic and secular values. "She fought for secularism, against all those forces seeking to divide the Indian people on lines of religion and caste. For her as Prime Minister there was but one religion, a sacred creed passionately held-- that all Indians were equal children of the motherland," the Congress president said in her speech.
Rahul Gandhi recalled his grandmother, whom he described as his mentor and guide. "I remember you Dadi with so much love and happiness. You are my mentor and guide. You give me strength. #Indira100," he tweeted.
Often described as the 'Iron Lady of India', Ms Gandhi was born on this day in 1917 in Uttar Pradesh's Allahabad.
(with inputs from agencies)