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Ms Williams, the first woman to lead the counter-terrorism unit, had the money stolen from her card when she used it to pay a restaurant bill, it emerged yesterday.
She became aware of the crime a few days later when her card was declined because she was over her credit limit.
A spokeswoman for Scotland Yard confirmed that criminals had made transactions using Ms Williams’s card but declined to go into detail.
“We are not prepared to discuss it because this is a private matter,” she said. “Ms Williams did identify a fraudulent transaction on her credit card. She reported the matter and it has now been resolved.”
Ms Williams, who is in her forties and joined the Metropolitan Police in 1982, became head of Special Branch in November 2003, and is in charge of 560 officers responsible for gathering intelligence on terrorist suspects and for protecting the Prime Minister.
Credit card fraud is one of the most common crimes in Britain, taking place once every eight seconds.
It rose by 20 per cent last year and cost British banks £505 million, although according to the Association of Payment Clearing Schemes (Apacs), skimming, when data from one credit card is copied to another, is becoming less common.
Sandra Quinn, the communications director at Apacs, said: “This type of fraud (skimming) is now on the decline because the introduction of chip and pin has limited the opportunity for people to get hold of your card. At the beginning of this year this type of card fraud had come down 29 per cent.
She said that people had been particularly vulnerable to fraud when using their card in restaurants and other places where the card may be taken out of sight.
“That happens less with chip and pin because the terminal comes to the table and you stay in control of your card,” she said.
“You are able to watch it the whole time. We estimate that more than 80 per cent of businesses now have chip and pin.”
Ms Quinn advised people to ensure that they always knew where their cards were and to check their bank and credit card statements carefully.
“Card fraud is impervious to who the victim is,” she said. “For the fraudsters, there is no personal contact with the victim. That means we’re all more vulnerable than we are from other types of fraud or other types of crime.”
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