Up to 10% of retailers' point of sale tills were not ready for today's (14 February) chip and Pin deadline imposed by the Association of Payment and Clearing Services.
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According to Apacs, 90,000 point of sale tills out of 860,000 in use in the UK at the end of 2005 could not authenticate payments using chip and Pin.
Retailers have been advised that when the customer has a suitable card they should only accept a Pin, but some retailers decided not to deploy chip and Pin before today's deadline because their existing electronic point of sale technology is hard to upgrade to the new verification system.
Some retailers were also reluctant because they did not want to disrupt existing technology refresh programmes to meet a deadline imposed by Apacs and the banks.
Others, including organisations processing low-value orders or taking online and telephone orders, had concluded that their existing technology fits their business processes more closely than the new system, an Apacs spokesman said.
Alex Tut, a consultant at Retail Systems Consultancy, said, "Bookmakers, for example, just do not have the need to have card authorisation integrated into their systems. It just does not work well because you are holding up your other customers."
Some larger retailers are also likely to miss the deadline for some of their stores. Waitrose only began to install a chip and Pin system in the new year after it cancelled the roll out of an interim system last November.
The retailer said problems with the hardware and software of the interim system were behind its decision to postpone chip and Pin last year.
The supermarket group said that 75% of its supermarkets had chip and Pin terminals one week before the deadline.