Chairman Sanjay Jhunjhunwala, who was facing a Red Corner Notice issued by the United Arab Emirates, was arrested after he returned from abroad.
The CBI had also issued a Look Out Circular against him.
Promoter Sandip Jhunjhunwala was also arrested by the agency here today.
The agency had registered a case against them and the Kolkata-based REI Agro, which deals with Basmati rice exports, in October 2015.
The action was taken on the complaint from a consortium of 14 banks led by UCO Bank.
It is alleged that the company cheated the banks using 150 shell companies, on the basis of fixed commission, through a group of brokers by creating false invoice, documents of money transfers for non-existent transactions, CBI sources said.
They said Jhunjhunwala was also facing a case of misappropriation of AED 160 million for which the UAE authorities had issued a Red Corner Notice against him.