The Congress alleged that the investigating officers "tampered" the hard disc of a computer seized from an accused in the case which, the party claimed, carried reference to the chief minister and several ministers.
"The CBI has many names and after what the CBI has said on Vyapam, its name now is Compromise Bureau of Investigation," Congress leader Kapil Sibal told reporters.
"It is unfortunate... in a country where investigative agency works one-sided and flouts the rule of law, what will happen to democracy there, one should think," Sibal said.
Sibal accused the CBI of "tampering" the hard disc.
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"It has now come to this level...we will now have to investigate the investigator. The Congress party will investigate it. We will all get together and charge-sheet them.
"We will file a private complaint in the trial court and ask the court to re-investigate. The accuser will become the accused now. The charge-sheeter has to be charge-sheeted," he said.
In a veiled threat to those behind giving clean chit to Chouhan in the case, the former Union minister said, "We are watching very carefully as to who is doing what. In the coming times, we also know who is doing what."
The charge sheet filed by the CBI in connection with Pre Medical test for 2013 has listed 490 accused which includes three Vyapam officials - Nitin Mohindra, Ajay Kumar Sen and C K Mishra.
The CBI charge sheet came as a major relief to the Madhya Pradesh chief minister as he had been given a virtual clean chit by the probe agency.
Nominated Rajya Sabha MP Tulsi, while referring to the CBI, alleged that he found it strange that "the black parrot which was caged, it now seems its neck has also been broken".
He said he has not seen a single case where over 50 witnesses have died, but the agency is unable to ascertain as to who were the beneficiaries of the money paid.
Sibal alleged several officers had been elevated by the government to higher posts in the CBI and the NIA disregarding complaints against them.
"We in the Congress party will now charge-sheet the one who charge-sheets others and will get together to tell the Madhya Pradesh court to do justice in the case," Sibal said.
The former Union Minister alleged that whenever it comes to Congress leaders, the CBI always targets them and it does whatever the government asks it to do. However, it never initiates any probe against the ruling party leaders, he alleged.
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