Air New Zealand chief commercial and customer officer Cam Wallace said a flight to Melbourne on Wednesday would operate as cargo only due to Australian travel restrictions.
A new poll released by News Corp's The Australian shows that Victorians are less satisfied with their state leader and his performance in handling the COVID-19 pandemic.
Flight NZ123 at 9.10am was cancelled, flight NZ6081, also at 9.10am, departed, and flight NZ127 at 2.10pm was cancelled.
On Tuesday evening Wallace said the company was awaiting government confirmation on the status of flights into Melbourne.
"We are very hopeful that Victoria will be able to bring their outbreaks under control but at this stage we can not possibly lift that border on 20 July as we were hoping to do", South Australia Premier Steven Marshall told reporters.
Victoria records 64 new COVID-19 cases on Tuesday when compared to 75 news infections reported on Monday.
People situated in postcodes 3038, 3064, 3047, 3060, 3012, 3032, 3055, 3042, 3021 and 3046 will be forced into lockdown until at least July 29 under stage three restrictions.
The airline was due to operate two return services to Melbourne on Wednesday.
Residents in the hotspot suburbs are now limited to only 4 reasons they are allowed to leave their homes: shopping for food and essentials, to provide care or seek medical treatment, to exercises, and to attend work or study.
Air New Zealand has been approached for comment about the Melbourne cancellations.