Resorthoppa and A2B Transfers have insisted their websites are secure following complaints posted online from customers claiming to have been victims of fraud.
The customer claimed their credit cards were used to make fraudulent transactions after booking with the sister transfer companies.
Clients writing on internet forums said hundreds of pounds worth of unauthorised payments, mostly to mobile phone companies, had been made in the months after they booked a transfer.
One post on the calis-beach.co.uk forum claimed: "I had £60 skimmed off my account this week.
“The only time this card has ever been used online was to pay for a Resorthoppa transfer. Seems too much of a coincidence."
Customers also shared their experiences on Trip Advisor and other sites. The issue appears to be mainly affecting people travelling to Turkey.
Matt Hall, managing director of Resorthoppa and A2B Transfers, said the company was investigating the clients' complaints.
He told Travel Weekly: "We are looking into it to see if there's an issue, but we don't believe there is a specific problem with our website. It could just be a co-incidence.
"This is only a very small minority of the three million passengers we carry a year. We don't believe there is anything to address, but we are looking into it."
A representative from the customer services team at Resorthoppa has posted on the Calis Beach site asking users to their booking reference to the team.
She wrote: "Our website carries 3D secure protection and is a safe, secure way of booking your airport to resort and resort to airport transfer.
"We have not been made aware of this issue occurring for other customers so would like to be able to look into the issues you have experienced and resolve them immediately."
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