CBI sources said Dixit, Kumar and Gupta were arrested late this evening after questioning during the day.
The case relates to alleged fraudulent exports worth Rs 8,000 crore, using inflated price tags, by Gupta in 2013-14 to companies based in Hong Kong and Dubai, CBI sources said.
They said the case was probed by Directorate of Revenue Intelligence.
It is alleged that garments purportedly exported were over invoiced to claim inflated duty draw back, the sources said.
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Based on its investigation, DRI allegedly asked Atul Dixit, a 1988-batch officer, and Nalin Kumar to block duty draw back claim of Rs 300 crore presumably made by Gupta, the sources said.
"It is further alleged that in order to favour the private person, the said public servants deliberately did not suspend the duty drawback of the firms immediately and ensured that the amounts claimed by the firms as duty drawback are transferred to their bank accounts," CBI spokesperson said.
They said the agency is probing alleged quid pro quo between Gupta and the Customs officers who did not act on the recommendations of DRI.
The sources said the searches were carried out at seven places here and one each in Gurgaon and Greater Noida at the premises of Dixit, Kumar and Gupta during which the agency recovered cash of Rs 85 lakh from the lockers of Kumar and property documents worth crores from Dixit's lockers.