Dominic Raab assured the firm's worried customers contingency planning is in place in the event the business cannot be saved.
His comments came as guests at a hotel in Tunisia report being locked in by security guards as staff demand extra money in fear it won't be paid by the holiday company and a union leader said employees are working for the firm while not knowing if they have a job or will even get paid for this month.
Thomas Cook is meeting with the firm's biggest shareholder along with creditors at City law firm Slaughter & May on Sunday in a final bid to piece together a rescue deal.
The travel company is at risk of falling into administration unless it finds £200 million in extra funds.
It was feared the collapse would leave up to 150,000 UK holidaymakers stranded.
But Mr Raab told the BBC's Andrew Marr Show on Sunday morning: "We have got all the contingency planning to make sure no one will be stranded.
"I don't want to give all the details of it because it depends on the nature of how people are out there, whether they have got a package holiday or whether they just paid for the flights and sorted out something separately."
He added: "But I can reassure people that in the worst case scenario, the contingency planning is there to avoid people being stranded."
Brian Strutton, general secretary of the British Airline Pilots Association, said lessons had not been learned from the collapse of Monarch Airlines in 2017.
"Thomas Cook is at the last chance saloon today and decisions about staff and passengers are being taken in secret. It's a much bigger scale than Monarch. There is a real risk that if the worst comes to the worst proper arrangements may not be in place for the repatriation programme and staff are still working while not knowing if they have a job or will even get paid for this month," he told PA.
He said the Government did not act on its own review which followed the Monarch collapse, adding: "This is a mess that could have been avoided. Ministers need to step forward and take responsibility for the sake of passengers and staff."
Thomas Cook reassured worried customers on Saturday night that their flights continue to operate as normal and all their package holidays are ATOL-protected.
However, tourists at the Les Orangers beach resort in the town of Hammamet, near Tunis, say their hotel is refusing to let guests leave while demanding extra money.
Ryan Farmer, from Leicestershire, told BBC Radio Five's Stephen Nolan the hotel had on Saturday afternoon summoned all guests who were due to leave to go to reception "to pay additional fees, obviously because of the situation with Thomas Cook".
With many tourists refusing to pay on the grounds they had already paid Thomas Cook, security guards were keeping the hotel's gates shut, refusing to allow guests out, or to let new visitors enter.
"We can't leave the hotel. I'd describe it as exactly the same as being held hostage," Mr Farmer said.
The Transport Salaried Staffs Association, which represents workers at the company, said the Government should be ready to assist with "real financial support".
General secretary Manuel Cortes called for an urgent meeting with Business Secretary Andrea Leadsom.
He said in a letter: "It is incumbent upon the Government to act if required and save this iconic cornerstone of the British high street and the thousands of jobs that go with it."
Shadow business secretary Rebecca Long Bailey said: "The Government faces a simple choice between a £200 million Government cash injection to save the company now versus a £600 million bill to repatriate UK holidaymakers."
It is understood that Thomas Cook has approached the Government in an attempt to plug a gap in its funding.
A Government spokesman said: "We recognise it's a worrying time for holidaymakers and employees.
"The financial circumstances of individual businesses are a commercial matter, but the Government and the Civil Aviation Authority are monitoring the situation closely."