Problems with the system started at the end of last week and have meant traders have not been informed by PayPal when online customers have ordered and paid for goods.
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This has led to customers having their payments debited from their accounts but not being sent any goods.
The bug has affected PayPal's instant payment notification system, reports The Register, with PayPal acknowledging the problem.
The problem is said to have been caused when PayPal administrators updated the instant payment notification (IPN) system.
PayPal was still trying to fix the problem at the weekend, and has not said how many traders have been affected.
Many eCommerce sites run on scripts that won't complete a transaction until an IPN is received from PayPal, which is owned by eBay.