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New Zealand had gone 102 days without community transmission of the virus until news of new Auckland cases were announced earlier this week. The rest of the country is currently at alert level 2.
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Four flights have already touched down in Queenstown this morning - with a total of 12 scheduled for the day.
In Dunedin, two Air New Zealand and one Jetstar flights are due to arrive and in Invercargill one inbound flight from Auckland is scheduled.
A reporter at Queenstown Airport said arrival numbers were small but the airport was "quite busy" with departures.
A passenger on a Jetstar flight said he was the "only one on the plane". He was returning home and had been in Auckland on business.
A second flight, an Air New Zealand one, had approximately 10 passengers on board, he said.
Airlines have made it mandatory for passengers leaving Auckland to wear face masks.
Queenstown Airport chief executive Colin Keel said yesterday that robust plans would ensure the airport could respond at short notice to changes in alert levels.
"We are working closely across the airport community, as we have throughout the Covid-19 pandemic, to ensure the appropriate protocols are in place and clearly communicated to the travelling public."
A cleaning and sanitisation programme at Queenstown Airport had increased in January and had continued since.
“Hand sanitiser stations are in place throughout the terminal.”
Invercargill Airport general manager Nigel Finnerty said seating had been adjusted at the terminal to reflect physical distancing requirements.
Signs had gone up reflecting the change to Alert Level 2 and cleaning of high-touch areas was intensive.
Dunedin Airport has increased cleaning at the terminal and 2m physical distancing is encouraged.