Sen, a critic of Prime Minister Narendra Modi, was chancellor of the university and his term had come to an end in July last year but he had continued his association as a member of its Governing Board.
Sources said President Pranab Mukherjee, in his capacity as the Visitor of the university, approved the reconstitution of the Governing Board in accordance with provision of the Nalanda University Act, 2010.
The President also approved giving temporary charge of Vice Chancellor to senior-most Dean of the University as the current VC Gopa Sabharwal's one year extension expires tomorrow. It will be a stop-gap measure until the new Vice Chancellor is appointed.
In February last year, Sen, in a letter to the Governing Board had said he will not seek a second term as Chancellor as the BJP government did not want him to continue.
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Trinamool Congress MP Sugata Bose and UK-based columnist Lord Meghnad Desai, who were also member of the GB, were not included in the newly-constituted board.
The new governing board will be a 14-member body which will be chaired by the chancellor. It will also comprise vice-chancellor, along with five members nominated by India, China, Australia, Laos PDR and Thailand.
The other members of the board will be Secretary (East) in the Ministry of External Affairs, an Additional Secretary rank official of Ministry of HRD and two members representing the Bihar state government.
While Sen could not be contacted for reaction, Bose, a former Harvard professor, said it was government's prerogative to reconstitute the board. But at the same time he said, "There was a need to ponder whether this is the way we maintain national prestige."
Reacting to government's decision, Singh said this is for the first time the governing board has been reconstituted in accordance with provision of the Nalanda University Act, 2010, adding it should have been done much earlier.
Indian government had enacted the Nalanda University Act, 2010 to implement the decisions arrived at the Second East Asia Summit held in January, 2007 in the Philippines and subsequently at the Fourth East Asia Summit in Thailand for establishment of the Nalanda University.
In 2007, the Nalanda Mentor Group (NMG) was formed to implement the project. The NMG was discharging the functions of the Governing Board.