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Thomas Cook customers may have to wait as long as two months to receive a refund for holidays they have booked with the collapsed travel firm.

The Civil Aviation Authority (CAA) said direct debit customers would be refunded within 14 days but others would have to wait up to 60 days.

The regulator said it had to refund 360,000 customers, three times larger than any previous refund programme.

The CAA said it planned to launch a new online refund system from 7 October.

The new system would provide “an electronic refund form”, said the aviation regulator.

“We hope to pay refunds within 60 days of receiving a valid refund form. More information will be available on our website from 7 October.”

The majority of Thomas Cook holidays are packages. Anyone who has bought a package holiday with Thomas Cook will be covered by the Air Travel Organiser’s Licence scheme (Atol). Customers entitled to a refund would have received an Atol certificate when they booked.

In total, 100,000 Thomas Cook customers paid for their future holiday by direct debit, with the remaining 265,000 using other payment methods.

In previous cases, where a holiday firm has collapsed, the refund process has typically taken 20-30 days, but the huge number of customers affected by Thomas Cook’s collapse and the possible risk of fraud is understood to have made the process much more time consuming.

Meanwhile, the CAA said it had now brought home over two-thirds of the people on holiday when the tour operator collapsed back to the UK.

It said there were still more than 43,000 people on holiday abroad due to return on or before 6 October.

“The scale and complexity of this operation will inevitably cause some inconvenience and disruption and I would like to thank holidaymakers for bearing with us,” said Richard Moriarty, chief executive at the UK CAA.