The Congress MLA said that as per media reports two men - Lucas Narzary(30) and David Islary(25) were shot dead on March 30 this year in an operation involving the Army, Assam police, CRPF and Sasashtra Seema Bal.
"The accusation of the two youths being killed in a staged or fake encounter has been levelled by none other than the Inspector General of the CRPF, North East Sector, Rajnish Rai," Saikia said in the letter.
He also pointed out that the Armed Forces (Special Powers) Act is in force in Assam and the Unified Command structure is also in place here.
"This means that the Union Home Ministry has a big say on security matters in Assam," Saikia added.
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The CRPF IG, a 1992-batch IPS officer of Gujarat cadre, said he had conducted a "discreet" inquiry on his own chronicling how a team of the Assam Police, the Army, the CRPF, its jungle warfare unit CoBRA and Sashastra Seema Bal conducted the encounter on March 29-30 at Simlaguri area of Chirang district.
Rai, in his 13-page report, had alleged that information about the incident and FIR filed by the joint squad of forces presented a "fictitious account" of the operation to "conceal pre-planned murders of two persons in custody and present it as some brave act of professional achievement".
The Union Home Ministry has acknowledged receiving the report and said it is being studied and action on its content will be taken soon.
Rai, deputy chief of CRPF formations in the north east, has also sent the report to the Assam chief secretary, who is the chairperson of the Unified Command of security forces, to the CRPF headquarters, the GOC of 4 Corps in Assam and to the director general of SSB.