The bureau has also charged some unidentified officials of the Staff Selection Commission (SSC) with issuing letters of appointment to the accused without verifying discrepancies in their admit cards issued for the examination for the posts, as per a copy of the FIR filed on March 6.
The copy of the FIR has been posted by the CBI on its website.
The selection process, which included a written exam and skill test, was conducted by the SSC between 2012 and 2014.
According to the FIR, the employees allegedly deceived the invigilators by bringing in dummy candidates for their exam.
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The accused allegedly inter-posed and mixed their photographs with those of the dummy candidates who appeared in their exam.
The accused also signed on their admit cards in a simplified way so that the dummy candidates could easily copy their signatures and appear in the exams in their place, said the FIR.
The FIR has been filed against two stenographers and nine multi-tasking staff members at the Income Tax office in Nagpur and a clerk posted at the I-T office in Jhunjhunu city of Rajasthan.
The 12 clerks and the unidentified SSC officials have been booked under IPC sections pertaining to forgery, cheating by impersonation, making false documents, and other relevant provisions of the Prevention of Corruption Act.
When contacted, a senior police official of the CBI's ACB here said the case was under investigation and refused to divulge any further details.
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