Mukherjee recalled Kurien's enormous contributions to the fields of agriculture, rural development and dairying.
Condoling Kurien's death, Vice President M Hamid Ansari said he was credited with being the architect of the largest diary development programme in the world-- Operation Flood.
"He engineered the white revolution in India and made India the largest milk producer of the world. He is recognised as the man behind the success of the Amul brand," he said.
The Prime Minister described him as an icon of India's cooperative movement and the dairy industry while Congress chief Sonia Gandhi said "we will always honour his memory and draw inspiration from his life work."
In his condolence message to Kurien's wife, Molly Kurien, the Prime Minister said Kurien's "contribution to the welfare of the farmer and agricultural production and development of the country is immeasurable.
Kurien was an icon of India's cooperative movement and the dairy industry," Singh said.
"His greatest contribution was to give a position of pre-eminence to the farmer and his or her interests rather than those of middlemen," he said.
Singh said he personally had a rewarding association with Kurien and benefited from his sagacity and vision.
Amul cooperative announced Kurien's demise on Twitter. "Sorry to inform that Dr. Kurien, father of White Revolution, passed away at 1.50 am," it said
Kurien had stepped down as chairman of the cooperative Gujarat Cooperative Milk Marketing Federation (GCMMF) which runs Amul in 2006.
Narendra Modi, chief minister of Gujarat where Kurien began cobbling together one of the world's largest dairy cooperative federations, said his "pioneering work gave the milk revolution, transformed India & touched us all".
Chief ministers, Governors and other prominent leaders too recalled Kurien's contribution in the nation's development.
Bihar Chief Minister Nitish Kumar said Kurien's passing away marks the end of an era.
The people of Gujarat and the country will forever remember him, he said in his condolence message.
Kurien had been decorated with innumerable awards including the Padma Vibhushan and the Ramon Magsaysay Award for community leadership.
Kurien, 90, passed away early this morning in Gujarat due to age-related problems.
Oommen Chandy, chief minister of Kurien's native state, and his cabinet colleagues, also expressed grief over his death.