The development comes after the Ministry summoned top IIT-Kgp officials last week to seek an explanation, sources said, adding the affidavit was withdrawn today.
They said the ball is now in IIT-Kgp's court to act fast against the professors before the ministry contemplates its next move.
The summoning of the officials last Thursday came after the anti-corruption watchdog had asked the ministry whether it was consulted by the premier technical institute before moving the high court.
Filing an affidavit before the Delhi High Court on March 20 in a case filed by whistle blower Rajeev Kumar, the prestigious institution sought dismissal of Kumar's plea on the ground of CVC's jurisdiction.
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"CVC does not have jurisdiction over the answering respondent (IIT Kharagpur)...," the affidavit filed by IIT- Kgp's registrar Tapan Kumar Ghoshal said.
Referring to the CVC Act, the institution said the "answering respondent (IIT) being an autonomous institute does not fall within any of the categories mentioned in the Act".
The corruption relates to the involvement of IIT top bosses for their alleged involvement in the Coalnet scam for computerisation of Coal India Limited and its subsidiaries between 2001 and 2004.