The case pertains to non-payment of dues by Flipkart to C-Store Company for laptops it supplied, officials at the Indiranagar police station here said.
They said an FIR has been registered against Flipkart's Sachin Bansal, Binny Bansal and a couple of company officials, based on the complaint by C-Store Companys Naveen Kumar.
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According to the complaint, C-Store had entered into a contract with Flipkart for the supply of laptops along with other electronic goods for its sale, and had supplied about 14,000 laptops, police said.
Flipkart, which returned about 1,480 units, did not pay for the remaining, the complainant said, adding that the other charges, including shipping had also not been paid.
The complaint alleges that there has been cheating to the tune of Rs 9.96 crore, police said.
A case has been booked under different sections of IPC, including cheating and criminal breach of trust, an official involved in the investigation said.
When contacted for it's reaction, Flipkart said it did not wish to respond for now.