Singh made the dig at Chouhan as the Congress stepped up its campaign against the BJP government in the state over the Vyapam scam by organising a state-wide bandh.
"Shivraj doesn't know the meaning of the term whistleblower and his proposed statewide yatra on the issue of Vyapam is an attempt to protect those involved in the scam," Digvijay told PTI.
The BJP state unit is planning to organise a yatra to be led by Chouhan over Vyapam scam in August, the date for which is yet to be finalised.
Significantly, the petitions filed by Digvijay and two whistle-blowers -- Dr Anand Rai and Ashish Chaturvedi -- in the Supreme Court had resulted in the apex court ordering a CBI probe into the high-profile scam.
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The state government had also requested the court to handover the probe into the scam to the central agency.
He demanded that all students accused in the scam be made government witnesses in the case as they were victims of middlemen.
"All those students who are accused in the scam should be made government witnesses as their parents were lured by middlemen into paying the money on the premise that nothing happens without shelling out rupees," he alleged.
"But the BJP government, in order to protect those involved in the scam, did not arrest those middlemen involved in it and instead arrested the students and their parents."
Singh said he had moved the Supreme Court as the BJP government allegedly tried to hush up the probe to save the big fish.
He also said he will press for a SC-monitored probe into the scandal and urge the court to handover the Dental and Medical Admission Test (DMAT) scam to the CBI as well for free and fair investigation.
The Association of Private Dental and Medical Colleges (APDMC) had recently cancelled the DMAT exam which was scheduled to be held on July 12, after the Madhya Pradesh High Court ordered to scan all OMR sheets of candidates.