The airline said while it "fully accepts it let customers down during the post-COVID restart", including with high cancellation rates, the Australian Competition and Consumer Commission case ignored the realities of the aviation industry.
All customers on cancelled flights were offered alternative flights or refunds with no "fee for service", Qantas said in a media statement on Monday.
The airline has filed its defence to the ACCC's case in the Federal Court.
The ACCC claimed the carrier advertised tickets for 8000 flights that had already been cancelled and that it engaged in false, misleading or deceptive conduct by selling the tickets for an average of more than two weeks.
It alleged Qantas didn't notify existing ticket holders for 10,000 flights that they had been cancelled for an average of 18 days, and up to 48 days, between May and July 2022.
Qantas cancelled a quarter of its flights between May and July 2022, which amounted to about 15,000, the watchdog said.
Airlines cannot guarantee specific flight times, Qantas said in its defence.
"As we've said from the start of this case, we fully acknowledge that the period examined by the ACCC was extremely difficult for our customers," it said.
"Restarting flying after the COVID shutdowns proved a challenge for the whole industry, with staff shortages and supply chain issues coinciding with huge pent-up demand.
"Qantas cancelled thousands of flights as a result and there were many unacceptable delays."
The ACCC case ignored the key condition that applied to ticket sales, which is that no airline can guarantee flights won't be delayed due to the nature of travel, including weather and operational issues, the airline said.
A full refund is offered to customers when a replacement flight cannot be arranged at no extra cost.
"This is consistent with our obligations under consumer law and is what we did during the period the ACCC examined," Qantas said.
All impacted domestic customers were offered same-day flights prior to, or within an hour after their scheduled departure times while 98 per cent of impacted international customers were offered options of flights within a day of the scheduled departure, it said.
Qantas also acknowledged that tickets were left on sale for longer than 48 hours in some cases but defended the action, saying "it does not equate to Qantas obtaining a 'fee for no service' because customers were re-accommodated on other flights as close as possible to their original time or offered a full refund".
Cancelled flights are now taken offline immediately, it said.
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