Mr Singh had dragged Mr Chouhan's name in the recruitment and appointment scam and alleged that data on the hard disk related to the case had reference to "CM", which was erased.
The central investigation agency, which filed a charge sheet in a Bhopal court two days ago, said, "There is no grain of truth in the allegation that the HDD (hard disk drive) seized on July 18, 2013 from the office of the then principal system analyst, Vyapam was tampered."
After the clean chit to Mr Chouhan, the state BJP said it is planning to file a defamation case against the former chief minister for levelling baseless allegations about tampering with evidence.
Mr Singh is on a pilgrimage tour of the river Narmada. The 70-year-old politician has embarked on 'Narmada Parikrama', a walk along the banks of the river.