They said the searches, launched at about 4pm, were being conducted in Mumbai, Pune, Surat, Hyderabad, Bengaluru and a few other cities against 13 companies linked to Choksi, his jewellery firm Gitanjali Gems and others.
Sources said the action was being undertaken to check the activities of some shell firms allegedly routing funds in this case.
PTI had first reported on February 18 that at least 200 shell firms and "benami" assets had come under the scanner of the investigative agencies probing the Rs 11,400-crore alleged fraud at the Punjab National Bank (PNB) that also involves Choksi's relative, billionaire diamond jewellery designer Nirav Modi.
A firm identified as Priyanka Gems Private Limited is also under the scanner of the department as are also some shell or bogus companies which do not carry out any business activity but have been used to conduct huge transactions in the past.
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"The raids are to collect documents and hard evidence. The action against shell firms is being magnified," a senior official said.
The department had recently attached the bank accounts and other assets of Choksi and the Gitanjali group.
Choksi, Nirav Modi and others are being investigated by multiple probe agencies after it recently came to light, following a complaint by the Punjab National Bank, that they had allegedly cheated the lender of Rs 11,400 crore, with the purported involvement of a few employees of the bank.
The Central Bureau of Investigation and the Enforcement Directorate have registered two FIRs each to probe the case.