For many years bricks-and-mortar stores have focused their anger on Amazon, whose rapid growth has done more than any other online retailer to undermine their businesses.
But the ecommerce giant had come onside as a supporter of the bill because it would have stopped states from singling it out as a target for tax collection.
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EBay and Overstock have led opposition to the bill from the internet sector.
Lobbyists for the retailers refused to throw in the towel, vowing to keep pushing the bill in this session. "Most Americans won't be taking the next two months off, and neither should Congress," said Jason Brewer of the Retail Industry Leaders Association.
In the Senate, a spokesman for Dick Durbin, a member of the Democratic leadership who helped pass the bill, said: "Our goal hasn't changed and the bipartisan group of senators and the coalition will continue to work to find a path forward for it."
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Retailers had hoped to attach the sales tax bill to a separate piece of legislation to extend a ban on the taxation of internet access – not internet sales – which both parties support.
Mr. Boehner's spokesman said: "The House and Senate should work together to extend the moratorium on internet taxation without further delay."