The Civil Aviation Authority (CAA) says it has now flown a total of 61,000 Thomas Cook customers back to the UK, taking the total to 40% of passengers.
On Thursday it used 69 flights to bring back 15,000 people as part of its repatriation scheme following the collapse of the holiday group.
Some 72 flights are due to operate on Friday to return 16,000 people.
The CAA says Operation Matterhorn will continue until 6 October with more than 1,000 flights planned in total.
The authority said 95% 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," said Richard Moriarty, chief executive of the CAA.