Flipkart, however, dismissed as "false and baseless" the complaint by the businessman.
The case pertains to 'non-payment' of dues by Flipkart to C-Store Company for laptops it supplied, officials at the Indiranagar police station in Bengaluru 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 Company's Naveen Kumar.
In a statement, Flipkart contended the complaint was "false and baseless", and denied "all the allegations and averments made in the FIR in entirety."
"Flipkart is exploring all available legal possibilities to safeguard its interests, including but not limited to initiating proceedings for defamation against the complainant.
According to the complaint, C-Store had entered into a contract with Flipkart for 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 registered under different sections of IPC, including those related to cheating and criminal breach of trust, an official involved in the investigation said.