A refunds website set up for Thomas Cook customers with future holiday bookings struggled to cope with the “unprecedented demand” as the final repatriation flight touched down in the UK.

What was described as the largest-ever refunds programme of its kind was launched by the UK’s Civil Aviation Authority on Monday – but many customers were initially left angry and frustrated after receiving error messages when attempting to submit their claims.

It also emerged that customers will have to wait for up to two months to receive their money back.

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Thomas Cook collapsed on 23 September, triggering Operation Matterhorn, Britain’s biggest peacetime repatriation mission.

The two-week operation has brought more than 140,000 people back to the UK and involved more than 740 flights using 150 aircraft from 50 partners around the world, with the majority of people flying on their original travel date. It concluded on Monday, with the final flight, from Orlando in Florida, touching down at Manchester airport with the last 392 passengers on board.

However, while the airlift is judged to have been a success, the huge reimbursement programme for those who had booked holidays failed to cope with demand after opening – prompting many customers to take to Twitter and other social media sites to vent their frustration.

The site will be used to refund more than 360,000 bookings for Thomas Cook Atol-protected holidays, covering trips that would have been taken by 800,000 people over the coming months. Atol (Air Travel Organiser’s Licence) is a financial protection scheme run by the CAA, and this is its largest-ever mass refunds programme.

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Some of the tens of thousands of people keying in their details on Monday morning were confronted with a message saying that “an unhandled fault has occurred”, while others were told: “Your claim has not been successfully submitted. Please try back again shortly.”

The problems were apparently still ongoing at lunchtime on Monday, with the CAA saying on Twitter at about 12.40pm: “We are receiving an unprecedented level of traffic to the website currently so please try again later if you are not currently able to get through the system.” The organisation denied that the site had crashed, and later in the afternoon it appeared to be working normally.

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Thomas Cook customers who were already abroad when the company collapsed can also claim for the cost of replacing the Atol-protected parts of their trip, or for out-of-pocket expenses incurred as a result of delayed flights.

The CAA said: “We aim to pay refunds within 60 days of receiving a valid completed claim form.”

Adam French, a consumer rights expert at Which?, said it was “understandably frustrating” for some customers that they were facing problems trying to submit their details because of high volumes of online traffic. He said: “It is vital that customers persevere and do not turn to alternative websites, as we’ve seen scammers seeking to take advantage of this situation by setting up convincing fake refund websites to fleece customers.”