Searches were being conducted at 50 locations, including New Delhi and Mumbai, for evidence of fraud carried out through the loan accounts of a company registered in the British Virgin Islands and a Finnish firm, the CBI said in a statement.
The case registered relates to criminal conspiracy, breach of trust by a public servant and cheating, according to the statement from the CBI late on Thursday.
The bank said in a statement it had sought recovery of assets from one borrower after it became a bad loan but it did not provide any details of loans to the other company or name the bank officials being questioned.
It said the CBI had been examining certain documents relating to that loan and had spoken to some senior officers.
According to the allegations, loans were granted to the companies by IDBI Bank's senior management and independent directors, who ignored existing guidelines and relaxed some of the conditions, the CBI said.
"It is a case of alleged fraud on the bank by then executives of the bank, then promoters of the group and the companies involved," the CBI said.
The alleged $90 million fraud, arose from losses resulting from two loans, according to the CBI. The statement did not say how much IDBI recovered from the borrowers.
The CBI also says IDBI gave the unnamed Finnish company a loan equivalent to 52 million euros ($63 million) in 2010. The firm was showing stress, and in 2013 it was granted voluntary bankruptcy by a Finnish court.
IDBI said in the statement late on Thursday it had given a loan to Axcel Sunshine Ltd in February 2014, which became a non-performing asset in December 2015.
"The loan has been fully provided for," IDBI said. "The bank has initiated recovery actions to recover dues from the borrower in August 2016."
Reuters was unable to contact Axcel Sunshine as no website could be found for the company.
The Finance Ministry asked all banks to step up vigilance following a $2 billion fraud in February at Punjab National Bank, the country's second-biggest state-run lender.
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