The case related to award of contract for the implementation of Enterprises Resource Planning Project in the public sector undertaking during 2004-09.
The agency has now named Natarajan and Coimbatore-based Astral Consultants' director C S Srivatsan as accused in the case of alleged tweaking of tenders in favour of the private company by the BEML.
According to the CBI probe, Natarajan and Srivatsan were part of alleged criminal conspiracy to award work worth Rs 40 crore to Astral Consultants.
Natarajan is already being questioned by the CBI in a separate case regarding alleged irregularities in procurement and supply of Tatra all terrain vehicles to army but he is not an accused in the case.
Teams of CBI officials reached the Bangalore-residence of Natarajan, residence of Srivatsan, besides Coimbatore office of Astral and took into their possession some "incriminating" documents related to the tendering process and communications exchanged with the company, CBI sources said.
Repeated attempts to contact Astral failed as the company did not answer phone call or respond to emails. Natarajan also did not respond to phone calls and messages.
"It is alleged that the accused persons were parties to a criminal conspiracy entered amongst themselves at Bangalore and other places during 2004-09 to cheat BEML in the matter of award of different works relating to the implementation of Enterprises Resource Planning Project in BEML causing wrongful loss to BEML and wrongful gain to others," CBI spokesperson said here.