IIT Kharagpur had suspended Kumar for "misconduct" in May 2011, the same year the Supreme Court had lauded him as an "unsung hero" for his efforts to reform the IIT Joint Entrance Examination (JEE), which has since been re-christened as JEE Advanced.
The institute set up a probe panel that found him guilty. In 2014, the IIT decided to hand him compulsory retirement.
Kumar, who alleged that the panel was biased, moved the Delhi High Court and obtained a stay on the IIT's decision. He also appealed to the then president requesting that the decision be quashed.
"Former president and Visitor of IIT Kharagpur has set aside the penalty of compulsory retirement on professor Rajeev Kumar...The institute accepts his technical resignation in view of the HRD communication following presidential order," an official memorandum said.
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Following the high court's stay order, Kumar had taken lien for two years and joined Jawaharlal Nehru University in 2015. However, he was relieved from JNU in June so he can join back at IIT Kharagpur.
The professor has appealed to JNU Vice Chancellor to reinstate him as his penalty has been quashed and resignation accepted.
Days before he demitted office last month, Mukherjee had ordered setting aside of the penalty imposed on Kumar.
The HRD Ministry had last week issued orders to the IIT Kharagpur director to comply with Mukherjee's decision.
Kumar was accused of "damaging the reputation of the institute" by levelling allegations on issues ranging from irregularities in the purchase of laptops to rampant copying by students during examinations.
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