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 today.
CBI 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 was alleged that the company had defrauded the banks to the extent of Rs 3,871 crore since 2013 through conspiracy, cheating and forgery, the spokesperson said.
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.