Thomas Cook customers hit by the travel firm’s collapse may have to wait as long as two months to receive a refund, according to the Civil Aviation Authority (CAA).

Direct debit customers will be refunded within 14 days, but others will have to wait up to 60 days, with 360,000 customers awaiting payment.

The CAA said this is three times larger than any previous refund programme, and on October 7 it will be launching an online refund system to cope with demand.

It said: “We hope to pay refunds within 60 days of receiving a valid refund form.”

Package holidays booked with Thomas Cook – the majority of its business – are covered by the Air Travel Organiser’s Licence (Atol) scheme.

The Leader: Thomas Cook customers may have to wait 60 days for a refund (Peter Byrne/PA)Thomas Cook customers may have to wait 60 days for a refund (Peter Byrne/PA)

Around 100,000 Thomas Cook customers paid for their future holiday by direct debit, with the remaining 265,000 using other payment methods such as credit and debit cards.

The CAA is responsible for bringing Thomas Cook holidaymakers home, as part of the biggest repatriation since the Second World War.

The costs are still being worked out by Government officials, but initial estimates suggest it will be double the £50 million it cost when Monarch Airlines collapsed in 2017.

The CAA said two-thirds of people on holiday have been brought home, with a further 43,000 due to return on or before October 6.

Other costs still unknown include the tab taxpayers will pick up to cover the unpaid wages and redundancy payments to 9,000 Thomas Cook staff who lost their jobs.

Last week, the Business Select Committee launched an inquiry into the collapse, demanding company bosses appear before them to explain what went wrong.

MPs intend to focus on executive pay and whether auditors did enough to hold bosses to account over their fondness for using “one-off” payments to flatter the underlying profits.

Business Secretary Andrea Leadsom has also launched a taskforce, although new reports have suggested she declined to speak with Thomas Cook bosses in the build-up to its collapse a week ago – as the company was desperately seeking a Government guarantee to satisfy its lenders.