The Civil Aviation Authority is investigating the failure of Middlesex-based Britain Travel after the firm ceased trading last week.
The CAA said it was working with an unnamed airline which is refusing to accept tickets issued by the agency.
Britain Travel has held an Atol since June 7 and sold both Atol protected and non-Atol protected flights through its Iata members.
The CAA said: “Although airlines normally honour scheduled tickets once issued, the CAA understands that some airlines are not accepting tickets issued by Britain Travel Ltd.”
The CAA said it had not been able to obtain any booking information from Britain Travel or its appointed administrator which meant it was unable to determine which consumers are protected by Atol.
Customers already overseas have been advised to speak to their airlines to find out if tickets back to the UK will be honoured.