The smartphone maker also said these online firms are not their authorised resellers.
"One, these e-commerce sites are discounting prices below what other retail stores would sell at. After that, if the customer faces any issues post purchase, they turn them away saying its a brand issue. This is hurting our brand," Gionee India Head Arvind R Vohra said.
While there is nothing wrong with selling phones at competitive rates, consumers not getting good after-sales service, he added.
When contacted, a Flipkart spokesperson said: "As India's leading e-commerce marketplace, we pride ourselves in offering our customers one of the largest selection of high quality and genuine products and brands along with a world-class customer service.
"We stand behind the quality and warranty associated with every product we list on our site. We can assure our customers that products on Flipkart are genuine and our customers will continue to enjoy the warranty and services extended to all original products as always."
In February, another Chinese player Lenovo had issued a similar advisory to its customers alleging the online portals were selling products at "very low predatory prices". It carried a list of all authorised stores and genuine partners on its website as part of its efforts to inform buyers.
A Snapdeal spokesperson said: "Only authorised sellers list their products on our platform. These authorised sellers, already selling offline, are the ones listed on our site and are selling Gionee products online through our platform."
Customers can rest assured that all products, including Gionee products which are available on Snapdeal are genuine and eligible for warranty, she added.
"Further, being an online marketplace, pricing decision solely lies with the seller listing the product," the spokesperson said.
Gionee, which last month claims to have sold 2.13 lakh handsets, said it has "zero-visibility" on sales through e-commerce sites, Vohra said.
"Their (e-commerce firms) way of doing business is hurting my business and has ramifications on the brand," he added.
Vohra clarified that Gionee does not have any direct arrangement with any e-commerce portal in India as of now and sells only through its e-store and registered distributors. It products are available across over 20,000 retail touch points.
"I would request customers to check all warranty and service related details carefully when they buy from e-commerce websites.
In a bid to woo customers, e-commerce companies offer heavy discounts on products, which are often below prices offered in the offline market.