E-commerce players will be required to deduct a certain percentage of the amount paid to the seller by the consumer for goods and/or services purchased by them through the platform, as tax collection at source (TCS).
The sellers can get this adjusted against their final tax liability.
However, small business owners, who usually operate with thin margins, may face working capital crunch due to this system, discouraging them from operating through these online platforms, said analysts.
Snapdeal co-founder and CEO Kunal Bahl said the issue needs to be "re-examined" and that "letter and spirit of the GST reforms need to be reflected in the implementation so that the current maze of compliance requirements is not unwittingly replaced with another set of fresh hurdles".
Terming the the provision as "discriminatory", industry body Nasscom said it can potentially render such e-commerce marketplace "unviable".
EBay India V-P and MD Latif Nathani said the government should not mandate pure-play online marketplaces to "front" compliance, disclosures and reporting obligations.
Flipkart, the largest e-commerce company in the country, said the passage of GST is expected to give a major boost to e-commerce in India.
Sreedhar Prasad, Partner (E-Commerce) at KPMG India, said under the 'destination-based consumption tax' concept, e-tailers will have to adapt to a new model wherein the state where the package is delivered gets the respective tax for the sale and not from where the order is booked.
Mahesh Jaising, Partner at BMR & Associates, said the destination-based consumption taxation will ensure all states get their share of revenue basis actual consumption.
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