Skippers Aviation says it has been left about $250,000 out of pocket after a Carnarvon travel agency went into administration.
More than 300 passengers who have booked flights between Perth and Carnarvon through the town's Travelworld branch may be affected.
They are being urged to apply for reimbursement from Consumer Protection's Travel Compensation Fund before re-booking flights.
Skippers' CEO Stan Quinlivan says the situation is disruptive to everyone involved.
"People in the community are getting together to try and get another agent up and running there," he said.
"There's a lot of people that have booked on other airlines that will probably lose money, and there's a lot of people that have booked overseas trips so it's a bit of a mess." Mr Quinlivan says passengers will lose their money and have to re-book.
"We can't refund the money because we never got the money," he said.
"And, if they're having some hardship, well, please talk to us in our reservations."