Addressing a function, he said students should be allowed to raise important research questions and break new grounds in scientific discoveries, artistic creativity and philosophical ruminations.
The president urged all to think about the future of Indian universities as a continuation of India's rich history and heritage of education.
"Let our universities of the future re-invent our rich past heritage of Kautuhalshala, hitherto silenced by the pedagogy of rote-memorising for test," Mukherjee said.
A Kautuhalshala is an assembly of inquisitive minds where questions are raised.
The president was speaking after receiving the first copy of the book 'Future of Indian Universities: Comparative and International Perspectives' from Nobel Laureate Amartya Sen who formally released it at the function held at Rashtrapati Bhavan.
The book has been complied by C Raj Kumar, Vice Chancellor of O P Jindal Global University.