The agency started searching his residence and offices in Kanpur from early in the morning, they said.
There were no arrests in the case yet, CBI spokesperson Abhishek Dayal categorically said.
He said Kothari, his wife and his son are being examined by the CBI, which is conducting the searches.
This is the second major financial scam to break out after the sensational Rs 11,400 crore fraud allegedly committed by billionaire jewellery designer Nirav Modi and his uncle Mehul Choksi, who is a promoter of Gitanjali group of companies.
Both fled the country before the Punjab National Bank realised the depth of the alleged crime.