The prime minister was speaking on the plane to New York for the UN General Assembly, moments before the news was confirmed that the 178-year-old travel company was going into administration.
Mr Johnson said the company’s request for a £150m bailout from the taxpayer was rejected because of the “moral hazard” it would create for other businesses to fail.
And he questioned whether action needed to be taken to stop the directors of travel companies escaping responsibility for rescuing their customers.
Stranded passengers will have their hotel and new flight bills paid for by the government's Civil Aviation Authority, funded through payments made by all airlines to a shared emergency fund as part of their licences to operate.
With the company on the brink over the weekend, some Labour politicians and trade unions had also called for comprehensive government aid to save the famous firm and its thousands of staff – pointing to the multi-billion-pound bailout of the banks a decade ago.
“It is a very difficult situation,” Mr Johnson said. “Obviously our thoughts are very much with the customers of Thomas Cook, the holidaymakers who now face difficulties getting home.
“We will try our level best to get them home – there will be plans ready to deal with that if it is necessary.”
But he added: “It is perfectly true that a request was made to the government for a subvention of about £150m.
“Clearly, that is a lot of taxpayers’ money and sets up, as people will appreciate, a moral hazard in the case of future such commercial difficulties that companies face.”
Hinting at action to stop a repeat of the fiasco, Mr Johnson said: “We need to look at ways in which tour operators, one way or another, can protect themselves from such bankruptcies in the future.”
“Clearly the systems that we have in place [must] make sure that companies such as Monarch or Thomas Cook don’t, in the end, come to the taxpayer for help.
“One way or the other, the state will have to step in, quite frankly, to help stranded holidaymakers.
“One is driven to reflect on whether the directors of these companies are properly incentivised to sort such matters out.”
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