All other Qantas or Jetstar customers with a flight cancellation will receive a credit to the value of their booking which is valid until the end of 2022.
''We're working with New Zealand authorities to ensure that our schedules align with available quarantine spaces,'' a spokesman said.
''We'd also like to remind passengers who are looking to book flights that they must have an allocated quarantine space before they purchase a flight.''
Qantas, which is marking its centenary with an special flight in Sydney on Monday, doesn't expect to resume most of its international flying until well into next year.
While passengers can enter New South Wales without having to quarantine that arrangement is not reciprocal and pressure on MIQ spots in this country is intense, especially in the leadup to Christmas.
There are 32 MIQ facilities across the country, with capacity for 6261 people at a time.
The new booking system introduced on October 5 caught some travellers off guard and they are now stranded overseas.