Officials, who have handled the files, have been asked to appear for examination and some of them have already been grilled, they said.
The sources said the agency has analysed the file movement records in the ministry and questioned the officials who had handled the files before it lost the trace in the maze of record rooms.
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The agency is also suspecting that some of the files may have been intentionally misplaced at the instance of some accused corporate groups.
The sources refused to reveal the identity of the officials questioned as they have not been considered as accused and the agency is yet to register any formal case which could only be done if some mala fide is found during preliminary enquiry.
The agency has registered two preliminary enquiries in connection with missing files after holding a meeting with the officials of Coal Ministry to reconcile the files which are not traceable and require a thorough probe by the agency.
The sources said during the reconciliation it became clear that 15-18 crucial files related to coal block allocations done in different batches are not traceable and it is affecting the agency's probe.
Based on the conclusions drawn during the meeting, the agency decided to split its enquiry in two parts-- files relating to allocations done during the period spanning from 2006-09 in which CBI has registered 13 FIRs so far and files related to the period between 1993 and 2005 in which no FIR has been registered, the sources said.