Qantas said menu changes mean vegetarian meals may not be available for passengers on some flights.
One passenger said he had been able to get vegetarian meals on Qantas flights since the 1990s.
The Qantas representative added that customers could still book special meals, including vegetarian and vegan food, on longer flights.
One frequent Qantas flier told The Guardian he had been able to get vegetarian options on flights in Australia since the 1990s.
The passenger, John Dee, accused Qantas chief executive, Alan Joyce, of alienating a "significant percentage of Qantas passengers" as around 10% of Australians had adopted a plant-based diet.