Chouhan has briefed his party president on various matters related to the scam and put up his stand in the matter, official sources said.
Chouhan's Delhi visit assumes significance in view of Parliament's monsoon session, which is beginning from Tuesday, and where opposition is all set to target the government over various issues including Vyapam scam.
Chouhan and Shah are understood to have discussed ways to counter the Opposition, which is also seeking the Madhya Pradesh Chief Minister's resignation over his alleged involvement in the scam, they said.
Chouhan is also understood to have shared the progress of the investigation being done by Madhya Pradesh Special Task Force in the scam, they said.
He was earlier scheduled to meet Shah at around 4 pm. He had flown for Delhi from Bhopal at 2.50 pm, but had to return due to bad weather. He later reached around 6.45 pm in a commercial flight.
He spent about four hours in Madhya Pradesh Bhawan before the meeting as Shah was at the Prime Minister Narendra Modi's residence, the sources said.
CBI has registered at least 12 cases so far, following Supreme Court's direction, to probe the scam.
Massive irregularities in various professional examinations and government job tests conducted by Madhya Pradesh Professional Examination Board or 'Vyapam' have been unearthed.
The first case in the scam was registered by the state police on July 7, 2013, at Rajendra Nagar police station in Indore.
At least, 55 cases have been registered by the state police and 2,000 accused have been arrested, they said.
Opposition Congress has alleged at least 49 people associated with the scam have so far died under "mysterious" circumstances.
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