Protx is the largest independent payment service in the UK, handling card payments for over 10,000 retailers.

The upgrade, originally due to be carried out in June, involved the implementation of a new system for repeat payments, recurring billing, delayed payments and processing of Maestro cards featuring 3D Secure technology.

But thousands of retailers were unable to take payments from 6 am on Wednesday following problems with the upgrade.

Protx says it became clear very soon after the live service was restored that the system was having problems processing payments.

"This led to transactions queuing and eventually this overloaded our payment gateway system leading to our system being unavailable," says Protx CEO Michael Alculumbre in a letter to the firm's merchant customers.

The problem was found to be caused by a table in the database that had not been indexed properly, he says.

Protx claims that its service was back online by 2.30 pm, but some merchants reported that technical problems continued throughout the day. Furthermore, retailers using the support forum on the Protx Web site were still reporting difficulties in accepting payments on Thursday.

In his letter, Alculumbre states that many merchants have not acted on information provided regarding 3D Secure for domestic Maestro card processing and the need to have a separate merchant account for mail order/telephone order (moto) and e-commerce transactions.

"Many merchants may have felt that the system outage lasted beyond 2:30pm because they had not applied the changes that we had informed them of over the last six months," says Alculumbre. "As a result these merchants may have been unable to process domestic Maestro transactions and/or transactions through the Protx virtual terminal, which many of our merchants use to process moto transactions."

Read Alculumbre's letter to Protx customers here: