He is understood have cleared the name of one Swapan Dutta as the pro-VC of the university, rejecting the one appointed by the HRD Ministry.
Senior professor of the varsity's Hindi department Chakardhar Tripathi's name had earlier this week recived the President's nod but the VC has chosen another academician for the post, said sources in the University.
They maintained the VC should have avoided holding such crucial meetings till the probe against him was completed.
Duttagupta could not be reached for comments.
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The HRD Ministry had recently launched a probe into alleged administrative irregularities against Duttagupta against the backdrop of questions being raised about his "autocratic style" of functioning in some quarters and by Congress MP Pradeep Bhattacharya in Parliament.
"The academic atmosphere has been thoroughly jeopardised and the Vice-Chancellor is functioning in an autocratic manner," the Congress MP had said in Rajya Sabha during a discussion.
He had accused the VC of appointing a Controller of Examinations despite having no powers to do so and sanctioned key posts in violation of the Visva Bharati Act.