On Thursday, the CAA used 69 flights to bring back 15,000 people as part of its repatriation scheme named 'Operation Matterhorn', the BBC reported
Some 72 flights were due to operate on Friday to return 16,000 people.
The CAA said that 'Operation Matterhorn' will continue until October 6 with more than 1,000 flights planned in total.
It said that 94 per cent of passengers have been flown home on the planned day of their departure.
"An operation of this scale and complexity will inevitably cause some inconvenience and disruption and I am very grateful to holidaymakers for bearing with us as we work around the clock to bring them home," the BBC quoted Richard Moriarty, Chief Executive of the CAA, as saying on Thursday.
Meanwhile, Thomas Cook staff were expected due to meet at the Manchester Airport on Friday as they planned to raise the topic of unpaid wages.
The latest data from the Insolvency Service shows that 6,000 Thomas Cook staff in the UK have been made redundant and just over 3,000 employees were currently retained.
The developments come after the British travel giant collapsed on Sunday after last-minute negotiations aimed at saving the holiday firm failed, the BBC reported.
The company had worked throughout last week to seek a compromise that would inject an additional 200 million pounds ($250 million) to the 900 million pounds it had already agreed.
( With inputs from IANS )