Sen, a Bharat Ratna awardee has withdrawn his candidature as the chancellor for a second term, saying the Narendra Modi government does not want him to continue in the chair, a contention rejected by the NDA government.
"Sen is a national treasure, and to be treated so shabbily is really unfortunate," Congress party spokesperson Ajoy Kumar said.
Another party spokesperson Sanjay Jha said "dumping" him from the university's chair was a "shame".
Historian and Trinamool Congress MP Sugata Bose said it's a "sad day" for the university and noted that Sen did not want to be chancellor but was requested and persuaded by the then UPA government.
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AAP leader Ashutosh also criticised the government, saying the incident shows that it (BJP) cannot tolerate any criticism.
"It is in the best interest of the country if the academia is kept out of politics," he said.
Industrialist Anand Mahindra also aired his view on the matter and urged Prime Minister Narendra Modi to ask Sen to stay on.
JD(U) sought President Pranab Mukherjee's intervention and urged him to seek explanation from the Modi government, which, it alleged, was increasingly "interfering" in the academia to "promote its ideology".
Sen, who has long been a critic of Modi, in a letter to the Governing Board of the University had said, "It is hard for me not to conclude that the government wants me to cease being the chancellor of Nalanda University after July, and technically, it has the power to do so.