The FIR was lodged by the state Economic Offences Wing (EOW) based on findings during investigation into a Civil Supply Corporation scam unearthed in 2015.
The newly-formed Congress government in the state on January 8 had set up a 12-member Special Investigation Team (SIT) headed by Inspector General of Police, Anti Corruption Bureau (ACB) and EOW, SRP Kalluri to probe the alleged multi-crore Civil Supply scam.
"The case was registered against then Additional Director General (ADG), ACB/EOW Mukesh Gupta and then Superintendent of Police (SP) ACB Rajnesh Singh Thursday late night, based on the complaint of Deputy Superintendent of Police (EOW) Anil Bakshi, who is a member of the SIT," a senior EOW official told PTI Friday.
Gupta is presently posted as Special DG at the Police Headquarters, while Singh as SP Narayanpur district.
As per the complaint, Bakshi during the investigation into the scam found that some important documents had been tampered with, the official said.
Dubey allegedly admitted to have committed the tampering, saying he was pressurised by Gupta and Singh,the official said quoting the complaint.
Dubey also revealed that the two senior officials wanted to show certain unlawful phone interceptions as legal, and therefore documents were tampered with and fabricated.
The two officers were booked under IPC sections 193 (false evidence), 201 (causing disappearance of evidence of offence, or giving false information to screen offender), 466 (forgery) and other relevant offences.
Further probe is underway, the official said.
Denying the charges against him, Gupta said all telephone interception were done lawfully and "with the approval of home department in every case".
"The SIT has deliberately ignored the records and FIR has been hurriedly registered on the basis of oral statements of subordinate officers taken under duress," Gupta said in a statement.
Meanwhile, R K Dubey, now DSP (EOW), on Friday approached the Chhattisgarh High Court, claiming that he was pressurised by the ACB chief to give a certain statement and sought protection citing threat to his life.
The high court observed that the state shall "proceed with the investigation in a fair manner and the petitioner is also directed to cooperate in the investigation, if any contemplated" while rejecting the petitioner's request for protection, Verma said.
The alleged scam was exposed in February 2015 when ACB and Economic Offences Wing (EOW) conducted simultaneous raids at 25 premises of Civil Supplies Corporation.
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