Sources said after detaining Kothari in Kanpur, the CBI is taking him to Delhi for questioning.
Earlier on Tuesday, the Income Tax department has attached 11 bank accounts in connection with the Rotomac bank fraud.
After questioning the businessman and his family members on Monday, the agency continued with its searches at Kothari's residence and offices in Kanpur on Tuesday.
The CBI has registered a criminal case against Rotomac Global Pvt Limited, its Director Vikram Kothari, his wife Sadhana Kothari and son Rahul Kothari and unidentified bank officials on a complaint received from Bank of Baroda.
The Bank of Baroda in its complaint said the conspirators cheated a consortium of bank loans to the tune of Rs 3,695 crore including the interest component.
The Enforcement Directorate has also registered a money laundering case against Kothari and his family members.
The loans the Kothari family is alleged to have defaulted on include Rs 754.77 crore (Bank of India), Rs 456.63 crore (Bank of Baroda), Rs 771.07 crore (Indian Overseas Bank), Rs 458.95 crore (Union Bank of India), Rs 330.68 crore (Allahabad Bank), Rs 49.82 crore (Bank of Maharashtra) and Rs 97.47 crore (Oriental Bank of Commerce).
This was the second major financial scam that came to surface after the sensation Rs. 11,500 crore PNB fraud allegedly committed by diamantaire Nirav Modi and his uncle Mehul Choksi.