According to the Civil Aviation Authority (CAA) Thomas Cook customers may wait for as long as two months to receive their refunds.
Customers who paid by direct debit will be refunded within 14 days whilst other customers will be waiting up to 60 days.
Currently there are 360,000 customers waiting for refunds, which is three times bigger than any other previous refund programme.
The CAA said that they are launching an online refund system which will start on 7 October.
They said, “We hope to pay refunds within 60 days of receiving a valid refund form.”