"We will still offer value for people but it is a cost we have to pass on; it's a cost we can't digest given what we have gone through."
It comes as Joyce also announced the airline will cut flights from some of its busiest Australian routes as it struggles to cope with the high fuel prices and staffing shortages at airports.
It will cut domestic capacity through to March 2023.
In a statement, Qantas said the impact on customers was expected to be "minimal" as flights would be removed "mostly from high-frequency routes".
"Those affected will be contacted directly with alternatives as close as possible to their original timing, usually within one to two hours," the statement read.
There are no changes to the carrier's international flights.
The airline has been able to recover the cost of high fuel prices in the international market through higher fares but has been unable to do so in the domestic market, Mr Joyce said in June.
Tourism expert Dr David Beirman said given Qantas announced an AU$1.19 billion dollar loss for the financial year 2021-2022 – on top of a more than AU$5 billion loss the year before – the airline, together with others, is not in any position to engage in long bouts of fare discounting in the foreseeable future.
"There were some cheap fares about in late 2021 and early 2022 to stimulate demand when travel began the big rebound after Covid restrictions were relaxed in Australia and internationally," Dr Beirman, from the University of Technology, Sydney, told news.com.au.
However, he said Qantas' need to peg back past losses, the added costs of rehiring workers let go during the pandemic and rising fuel costs amid Russia's invasion of Ukraine, makes it all but "inevitable" airfares will rise and fuel prices will remain high this year and possibly into 2023.
"Alternative fuels, which are being sought by any airlines including Qantas, may present a slim chance of addressing fuel prices in the medium to long-term," Dr Beirman said.
"But I think it's likely that all those millions of people who are keen to resume air travel are more than likely to find it more expensive in 2022 and 2023 than in the pre-Covid years."
Dr Beirman said one thing that all airlines are acutely aware of is that fuel is the biggest cost component for airlines.
"[It] accounts for 40 per cent of costs for full-service carriers like Qantas and over 50 per cent of costs for low-cost carriers like Jetstar."
Following Qanatas' announcement of a new route from Australia to New York – via Auckland, Dr Beirman said the possible reason the airline is keen on long-haul flights is fuel costs per kilometre are lower than short-haul domestic flights.
"In simple terms, the longer and higher they are in the air, the less fuel they consume per kilometre. Take-offs and landings really chew up the fuel."