CAA chairwoman Dame Deirdre Hutton told BBC Radio 4’s Today programme on Wednesday that the authority had issued guarantees to the 3,000 hotels with Atol-protected British tourists.
When it was suggested the total owed by Thomas Cook to hotels was £338 million, she said: “Yes, we have learned of one hotel in Mexico that is owed £2.5 million, so it is hardly surprising they are worried. That hotel is working very closely with us, which is great.”
Dame Deirdre added: “It’s very distressing for people who are finding difficulties with their accommodation.
“We have got more than 200 staff working here together with Thomas Cook staff and we have already started making the first payments. But, as you say, given how much those hotels are owed by Thomas Cook, it is hardly surprising that they are suspicious and angry.”
Some holidaymakers had earlier claimed they had been prevented from leaving Cuba without paying extra for their hotel stays, but they have now been told they are free to leave.
The British ambassador to Cuba said hotels had been instructed to allow customers to leave without paying additional charges.
Antony Stokes tweeted: “Urgent for #ThomasCook customers: hotels in #Cuba now have authority/instruction to allow customers, and air crew, to depart without paying (on basis of ATOL guarantee).
“Very grateful for patience of all affected in distressing circumstances.”
A government minister admitted the cost of bringing Britons back home could be around £100m.
Transport Secretary Grant Shapps added: "The final cost of repatriation for the Monarch situation was about £50 million, including Atol contributions.
"The repatriation efforts for Thomas Cook is now known to be about twice the size and more complicated."
He told MPs that bailing out the troubled travel firm would have been "throwing good money after bad" and said efforts were being focused on repatriating Britons.
Union leaders stepped up calls for the Government to intervene in the crisis after news that the German airline subsidiary of the travel giant is being given finance to help secure a rescue deal.
Condor is being given six months financing by the German government, worth a reported £350 million, to continue to operate.
But in Poland, Thomas Cook’s unit Neckermann Polska said on Wednesday it was filing for bankruptcy.
The announcement by the company’s president Maciej Nykiel came with about 3,600 people booked on holidays with the company outside Poland.
Thousands of UK workers have lost their jobs and face a battle to receive any redundancy pay after Thomas Cook went out of business on Monday.
Brian Strutton, general secretary of the British Airline Pilots Association (Balpa), said: “Good luck to the Condor staff and customers, but with UK holidaymakers stranded and 9,000 staff out of a job, the Thomas Cook directors need to explain why the UK airline had to be closed but the German one was allowed to continue to operate.
“And why couldn’t the UK Government give the same kind of bridging support as the German government when it was well known that Thomas Cook had a Chinese buyer lined up? It’s a national scandal.”
Dame Deirdre told the BBC that despite concerns about Thomas Cook it was a private company and it was down to the directors to decide when it could no longer “operate solvently”.
She added: “The problem with Thomas Cook is it has been struggling for years.
“Mostly I think struggling to modernise itself. It’s not working in a sort of barcode age way and we have been increasingly concerned about it.
“But it’s a private company, a listed company, it’s up to the directors to decide when they can no longer continue to operate solvently.”
The CAA said it had completed more than 130 flights on Monday and Tuesday returning almost 30,000 people back to the UK, with 95% flying back on the day of their original Thomas Cook flight.
It added that it was working “around the clock” to bring an estimated 120,000 passengers back to the UK, with 70 flights with seats for 16,500 people planned for Wednesday.
A Department for Transport spokesman said: “The German airline Condor is a different airline, operating in a different market, and with potentially different commercial prospects. It is therefore a decision for the German authorities whether they agree to support German businesses with short-term taxpayer loans.
“The Government was not presented with a viable proposition by Thomas Cook’s board to support the company. We stand fully by our decision.”