The president added that India could be a world leader in education if "we discover the will and leadership to take us to that pinnacle".
Addressing a conference of vice chancellors of central universities at Rashtrapati Bhavan here, the president said: "Education is no longer just the privilege of the elite, but a universal right."
The conference was attended by Prime Minister Manmohan Singh and vice chancellors of 40 universities.
Mukherjee said most central universities continue to suffer from an acute shortage of faculty.
The vacancy figure had fallen from 6,422 last year to 4,784, showing that just 25 percent of the vacant posts had been filled up.
Mukherjee expressed concern over the absence of Indian universities
The president said that during the past 18 months he had visited 58 institutes of higher education, including 17 central universities. These institutions had a huge potential which was untapped, he said.
The central universities should be the "launchpads of innovative ideas and institutionalise structures that can identify ingenuous ideas and mentor them into viable products", a Rashtrapati Bhavan statement quoted him as saying.
He said the National Mission on Education through Information and Communication Technology (NME-ICT) and National Knowledge Network had connected 1,163 institutions and urged the remaining universities to become a part of this e-family quickly.
He called upon the universities to effectively use the ICT networks for imparting quality education.
The president urged the human resource development ministry, the University Grants Commission and the central universities to jointly take action to improve the governance system and structures.
Mukherjee expressed concern over the absence of Indian universities in the ranking of top universities in the world.
He asked the universities to appoint a nodal authority to present their achievements to the ranking agencies in proper perspective.
Alleging "grave" indiscipline by students and staff in some places, he said maintaining discipline in campuses should be the highest priority of authorities.
Only then "an environment where students can study and research without stress or fear can be created", Mukherjee said.