The Which? Web Trader initiative was launched in July 1999, and was one of only three UK trust schemes to be given government backing, but it is being pulled because of costs, the Consumers' Association said.
The UK has the highest percentage of regular online shoppers in Europe, with 54% of those with Web access making purchases online, claimed analyst group Forrester.
Last month more than £1bn was spent online in the UK, according to retail analyst organisation IMRG
However, Paul Kitchen, head of online at the Consumers' Association, said there was still work to be done to boost confidence in Internet shopping.
"There is still a need to increase consumers' confidence about shopping online and it is now up to business and government to set up an alternative scheme to build on the successful work of Web Trader," he said.
The Consumers' Association allowed online retailers to display a Which? hallmark after they had carried out a self-certification exercise. Those using the scheme include Carphone Warehouse, Debenhams and EasyJet.
"Since Which? Web Trader launched three and half years ago, it has received more than 8,000 applications from e-traders, of which 2,700 were accepted, and has successfully resolved over 2,000 disputes on behalf of consumers," said Kitchen.
"But providing such an effective and well monitored code costs a significant amount each year and we need to use our resources in the most efficient way possible."
The scheme has not escaped controversy during the past three years. In February 2001, research revealed that nearly a quarter of the participants in Web Trader had failed to display a privacy statement telling customers how personal details were stored and distributed - one of the key criteria required to display a Which? hallmark.
At the time, Kitchen admitted that only 388 of the 1,333 Web Trader members were fully compliant with the criteria, which included pricing, payment, refunds, contracts, guarantees, advertising and complaints handling.
In June 2001 the Consumers' Association was left red-faced after it emerged that its TaxCalc Web site had allowed credit card details of 2,700 customers to be exposed after a security breach, was not part of the Web Trader scheme.