"I must convey my sense of dismay on seeing a recent report that not a single Indian university, including the premier Indian Institutes of Technologies (IITs), featuring in the 200 top-rated universities in the world," said Mr Mukherjee on Saturday in his address at the 58th annual convocation of IIT-Kharagpur.
"You may question the report but for me the important question is why are we - a rising economic superpower - not able to promote our standards to be rated indisputably among the top 10 or even top 50 or 100," he said.
The President, accompanied by Civil Aviation Minister Ajit Singh - an alumni of IIT Kharagpur, took part in a function marking the culmination of the institution's Diamond Jubilee celebrations.
However, West Bengal Chief Minister Mamata Banerjee was conspicuous by her absence. She later took part in a protest rally in the city demanding rollback of hike in diesel prices and FDI in retail.
Welcoming IIT-Kharagpur's 'Vision 2020' - to be in top 20 global education institutes by the year 2020, Mr Mukherjee urged other premier Indian educational institutes to follow suit.
"To realise our true potential it is necessary to start now with the urgent task of developing in our students a scientific temperament. It is necessary to design and develop, without delay, advance technology at competitive cost which would be a boon for our industry, trade and commercial sectors," he said.
Stressing on the need for adaptation and application of new technology to Indian conditions and requirement, Mr Mukherjee said the same would open up new market opportunities and these must be made "an integral part of the courses that our students attend".
He strongly recommended "more collaborations, exchanges and cross-pollination of ideas with the best minds in India and abroad" and asked the IITs to take the lead in ensuring "continuous revitalisation of institutions through research, experimentation and innovation".
Describing the younger generation as "critical to the development of the society and nation", the president urged them to "learn more, explore and contribute more".
"I would expect you to channelise your creative energy to contribute in an exceptional and significant way towards the nation's goal of achieving intrinsic growth and sustainable development of all strata of the society," was Mr Mukherjee's appeal to the passing out batch.
The President also praised the IIT Kharagpur for its initiatives of establishing new postgraduate programmes in Energy Engineering, Nano Science and Technology, as well as setting up a School of Bioscience and a School of Environmental Science.