Prasad, a 1983 batch IAS officer of Tamil Nadu cadre, was due to retire on May 31.
Prasad, an Additional Secretary in the Home Ministry, is granted extension in service for a period of two months with effect from June 1, 2016 to July 31, an official order said without mentioning the reason behind it.
Official sources said the extension has been given to help the Home Ministry decide on future course of action on the findings of the one-man probe panel headed by Prasad. The report is to be submitted before this month end.
Following an uproar in Parliament in March this year, the Home Ministry had asked Prasad to inquire into the whole matter.
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The papers which disappeared from the Home Ministry include the copy of an affidavit vetted by the then Attorney General and submitted in the Gujarat High Court in 2009 and the draft of the second affidavit, also vetted by the AG, on which changes were made by the then Union Home Minister P Chidambaram.
Two letters written by former Home Secretary G K Pillai to the then Attorney General late G E Vahanvati and the copy of the draft affidavit are also missing.
Prasad was recently embroiled in a controversy after an Under Secretary in the Home Ministry's Foreigners Division accused him of pressuring him to give clean chit to Ford Foundation, which allegedly violated provisions of the Foreign Contribution Regulation Act. Prasad has denied the allegation.