UGC Joint Secretary Rajesh Anand, who is at present under suspension, was issued the notice for dismissal from service on May 27 and has been given 15 days to reply.
It is learnt that the decision to issue termination notice to Anand was taken on May 20, after the Commission examined the charges and allegations against him.
A complaint had also been forwarded against him by Union Minister Maneka Gandhi when she was an MP, sources said.
As per the UGC charge sheet issued in April 2014, Anand was accused of directly writing to the Prime Minister making sarcastic remarks about UGC. He was also accused of approaching MPs to write to the Prime Ministers and others against UGC authorities, bypassing the available channels and ignoring norms and discipline.
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Another allegation faced by him was of manipulating names of Expert Committee for evaluation of proposals of new colleges and mislead the higher authorities.
Claiming that the action taken against him was "not fair", Anand said it was he who had tried to expose irregularities in UGC, the country's apex higher education regulator.