Thomson and First Choice have cancelled flights to Luxor for the rest of the summer, blaming a fall in demand.
The operators apologised to customers booked to travel on the weekly flight from London Gatwick.
"We understand for customers booked to travel to Luxor, this news will be very disappointing and we apologise for any inconvenience caused," it said.
"All customers will be contacted directly and provided with a full refund or will have the option of transferring their holiday to an alternative destination."
A forum has been set up on TripAdvisor by affected customers, some of whom say they have not yet been contacted.
Cyplon Holidays says it is being inundated with calls from customers impacted by the decision.
It is reassuring travellers they can re-book on flights with Egyptair from London Heathrow, which fly daily via Cairo and direct to Luxor on Mondays.
The decision by Thomson and First Choice comes weeks after a suicide bomb attack at a popular tourist site in Luxor.
The Foreign and Commonwealth Office did not change its advice to Egypt following the attack.
