In his acceptance speech, Mukherjee underlined that in global rankings, educational institutes of the region do not figure.
He said it is not due to a lack of talent in students or faculty but because "certain technicalities" need to be worked upon.
Mukherjee, a history aficionado, said the region which was known for institutions like Taxila and Nalanda has lost its sheen over the years.
"There is close connection between research and industrial development," he said.
Prime Minister Pushpa Kamal Dahal 'Prachanda', who is the Chancellor of Kathmandu University, conferred Doctor of Letters (D.Litt) to Mukherjee in recognition of his outstanding contribution in Public Relations, regional cooperation and international relations.
Earlier, Mukherjee, who is on a three-day state visit to Nepal, started his day by offering prayers at the historical Pashupatinath Temple.
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