The agency, which filed charges against 490 people, said a hard disc that Congress' Digvijaya Singh had alleged was tampered to erase references to the chief minister, had not been tinkered with.
The Supreme Court had ordered a CBI probe in 2015 at a time Mr Chouhan was under intense pressure from rival sections within the party and the opposition Congress that linked a spate of more than 30 deaths to the Vyapam scam. This list included a journalist tracking the case Akshay Singh and the then Governor Ram Naresh Yadav' son Shailesh.
The long list of accused charged by the CBI on Tuesday, however, only includes 3 officials of the Madhya Pradesh Professional Examination Board (Vyapam), 17 middlemen and "three racketeers" who engineered the scam.
These people ensured that aspirants who paid money to clear the 2013 pre-medical test were seated just behind the assigned 'solver', also enrolled as a candidate who would let the beneficiary copy the answers. There were also reports of imposters writing the examination for candidates for a fee or candidates leaving the answer sheet blank which were written at a much later stage.
A CBI statement said 297 beneficiary and solver candidates and 170 guardians of the candidates had been charge-sheeted. The CBI is also going to file charges against 12 minors in a juvenile court.
"I am the whistle-blower in the Vyapam scam, I found discrepancies and so ordered STF (special task force, or special team) probe," he told NDTV after the top court ordered the probe in 2015.
It is around this time that Mr Chouhan was considered to be politically vulnerable and faced jabs from within the party as well. The state's Home Minister Babulal Gaur, who Mr Chouhan had replaced in 2005, had said he would have advocated a CBI probe much earlier if the Chief Minister had consulted him.
Speaking against the backdrop of a series of deaths, another party colleague, Uma Bharti, told news agency PTI that she was a minister "but still I am scared. I will convey my fears to Shivraj Singh Chouhan".