The apex court also directed CBI to file the remaining over 30 charge sheets in connection with the scam within three months.
A bench of Justices Ranjan Gogoi and N V Ramana said that all the allegations and counter-allegations can be raised before the trial court and there is no need for it to go into the CFSL report filed by CBI in a sealed cover.
While disposing of the pleas including that of senior Congress leader Digvijaya Singh, the bench said that it will not take into consideration the remarks made by the high court against him.
The bench told senior advocate Vivek Tankha that these were the prayers in the plea filed by Singh, which now stand addressed as CBI has now filed the CFSL report.
"If there are any further grievances with regard to trial of the cases, they can be raised before the subortinate courts," the bench said.
The apex court was hearing a batch of petitions including one filed by Digvijaya Singh seeking monitoring of the probe into all cases arising out of the Vyapam scam.
The scam relates to alleged irregularities in the Madhya Pradesh Professional Examination Board, which holds exams for positions like medical officers, constables, teachers and auditors for government departments.
The Madhya Pradesh government had given its consent to shifting of the investigation from the Special Investiation Team (SIT) and the Special Task Force (STF) to CBI.
Singh and whistleblowers -- Ashish Kumar Chaturvedi, Prashant Pandey and Dr Anand Rai-- had moved the apex court seeking a CBI probe under its supervision.
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Meanwhile, Madhya Pradesh Chief Minister Shivraj Singh Chouhan claimed in Bhopal that CBI had told the apex court that electronic evidence in the case had not been tampered with.
"I have got the information that investigators have found no tampering (with hard disk and pen drive)," he told reporters.
State BJP chief Nandkumar Singh Chouhan said that Congress leader Digvijaya Singh wasted the Supreme Court's time by levelling false allegations.
State Congress, however, said that BJP was misleading the people.
"The examination report of Hyderabad laboratory about hard disc tampering is yet to be opened by the Delhi High Court," said K K Mishra, state Congress spokesperson.
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