Mr Misra's aides were arrested two days after the cross-voting in the state assembly.
Two former secretaries of senior BJP leader Narottam Mishra, ex-water resources minister in the Shivraj Singh Chouhan government, were arrested by the Economic Offence Wing of the state police on Friday in the alleged Rs 80,000 crore e-tendering scam.
The arrests of Mr Misra's aides - Virendra Pandey and Nirmal Awasthi - are the first arrests in the case which are directly linked to a former minister.
After they were taken in police custody, both of them were admitted to a hospital late night after they complained of chest pain.
The two aides were interrogated in the case on Wednesday. They were also questioned in the case last month for 10 days.
Mr Misra's aides were arrested two days after the cross-voting in the state assembly.
On Wednesday, Sharad Kol and Narayan Tripathi - both former Congressmen - voted for the Congress's Advocate Protection Act Bill - a longtime demand of the lawyers of Madhya Pradesh. The bill, drafted 15 years ago, had never made it to the assembly during the three-term government of Shivraj Singh Chouhan.
After the cross-voting, which came as a rude shock to the BJP, Mr Misra had said: "The game has been started by the Congress, but will be ended by us." In the past, the Congress has accused Mr Mishra of trying to topple the Kamal Nath government by making offers to Congress and the allied legislators.
The e-tendering case pertains to the alleged tampering of an e-tender floated by the Water Resources Department in 2018. The department had floated Rs 116-crore e-tender for a project that a Gujarat-based firm, Sorathia Velji Ratna & Company, bagged for Rs 113 crore. When the letter of acceptance was given, the amount was reduced to Rs 105 crore, sources in the EOW in the Bhopal headquarters told NDTV.
The first information report or FIR in the alleged scam was filed in April, nearly 11 months after the EOW registered a preliminary enquiry (PE) into the matter in May last year.
The e-tendering scam was first flagged by Madhya Pradesh Jal Nigam's Tender Opening Authority PK Guru who received an error message on March 3, 2018 on the e-procurement system saying: "the content has been modified". He received the message a few hours before the tenders worth around Rs 600 crore were to be opened in Bhopal.
Madhya Pradesh State Electronic Development Corporation (MPSEDC) is the nodal agency that hosts the e-procurement and tendering portal of the state government. The MPSEDC entered into a tripartite agreement with TCS and its consortium partner Bangalore based Antares Systems Limited on January 1, 2013 for customization, integration, data migration, implementation and maintenance.
In March last year, MPSEDC Managing Director Manish Rastogi wrote to the TCS and Antares to inquire into the "the content has been modified' message received by PK Guru.
Mr Rastogi, based on these findings, wrote to the concerned authorities for cancellation of the nine allegedly rigged tenders following which all of them were cancelled. State chief secretary marked the findings to the EOW, directing it to register a case. A PE was registered.
Mr Rastogi, however, was later transferred out of the MPSEDC.
According to an estimate, tenders worth over Rs 80,000 crore have been awarded to various companies through the e-tendering process after the January 2013 tripartite agreement.