The Competition Commission of India (CCI) in January ordered a probe into alleged violations of competition law and certain discounting practices by the two e-commerce giants, but a state court put the investigation on hold last week following a challenge by Amazon.
Flipkart has filed the case in a court in Bangalore aggrieved by the CCI's probe order.
In the case Flipkart argues that CCI ordered its probe without initial evidence that the company's practices were harming competition.
The filing comes days ahead of U.S. President Donald Trump's visit to India, and amid U.S. concerns about India's tightening of foreign investment rules for the ecommerce sector.