In a letter to the HRD Ministry, CVC has directed it to provide a copy of the affidavit, sources said.
IIT Kharagpur had last month claimed it is an autonomous body and the corruption watchdog has no jurisdiction over it after CVC directed the Centre to initiate action against three IIT professors for their alleged involvement in a scam.
The development came as the Ministry today summoned top IIT Kharagpur officials to seek an explanation.
"CVC does not have jurisdiction over the answering respondent (IIT Kharagpur)...", the affidavit filed by IIT- KGP's registrar Tapan Kumar Ghoshal said.
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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 affidavit had come just days ahead of the institute's Board of Governors was due to meet to respond to CVC's direction to the ministry and the institute to initiate major penalty proceedings against three IIT professors indicated in Rs 40 crore Coalnet scam.