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Direct flights into Auckland from Dunedin, Invercargill and Queenstown are suspended from today while Auckland remains under Covid Alert Level 3.
Air New Zealand confirmed it would operate a reduced domestic schedule to and from Auckland.
The only airport in the South Island with direct flights would be Christchurch with 13 weekly returns.
"The changes to our network relate to flights to and from Auckland. The remainder of the network is unchanged," an Air New Zealand spokeswoman said yesterday.
Invercargill Airport general manager Nigel Finnerty said there were "no flights planned again until after the 26th".
"While it is disappointing we are losing the Auckland flights for a couple of weeks, we certainly understand the response to Covid-19 is the most important thing at the moment. And obviously we are supporting that."