Under TCS, e-commerce marketplaces will have to deduct a portion of the amount payable to sellers on their platform and remit it to the government.
The companies said this would result in a capital lock-down of about Rs 400 crore per annum and also discourage merchants from selling online.
The draft model GST law is due to be finalised at the end of this month.
"We believe we have made a significant difference to the whole ecosystem... There are hundreds and thousands of sellers online and a lot of them are entrepreneurs, some of them are offline retailers... We have come a long way in creating this ecosystem," Flipkart co-founder Sachin Bansal told reporters here at a FICCI event.
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"This is apart from the TCS issue. Our estimate is that at current scale, Rs 400 crore per annum of capital will be locked into the system that will not be accessible to sellers and will eat into the working capital of the sellers and will deter them from coming online and listing with us," he said.
The three companies -- which are locked in intense competition for leadership of the booming Indian e-commerce market -- have come together for the first time to voice their concerns on an industry issue. They, in fact, have taken potshots at one another on social media platforms like Twitter and offline.
The companies contended that the clause, therefore, is detrimental towards e-commerce companies that have brought in billions of dollars of investment.
"All of us are investing ahead of scale and a lot of the investment is going into building the right infrastructure and ecosystem, in training/educating sellers and bringing them online and that attracts consumers to come to our marketplaces... This flywheel has been spinning for the last few years... When the ecosystem gets excited, a lot of other industries benefit," Amazon India Head Amit Agarwal said.
Snapdeal co-founder and CEO Kunal Bahl said "e-commerce is vociferously for GST.
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