Flights at Queenstown and Dunedin airports are up and running again after a day of diversions and cancellations due to strong winds and wild weather.

Among the affected were the Highlanders, whose flight from Dunedin to Christchurch had been cancelled ahead of their Saturday night game against the Crusaders.

Dunedin Airport chief executive Richard Roberts said the team was due to make an 11am flight out of Dunedin.

Parts of the airport had gone underwater overnight, in what airport staff were calling the worst flooding they'd seen in 20 years, he said.

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Roberts said there would be superficial damage to hangars and rental car buildings.

"It's amazing that we survived," he said.

"It's still raining and we're sitting there monitoring all the pumps, waiting for the rain to stop and then it will be a clean-up job.

"Some of the rescue fire boys have been there through the night and we've got other staff coming in now, and they're just looking after people in the terminal."

Queenstown Airport spokeswoman Jen Andrews said the first flight of the day had landed from Auckland at 8am - the first to land at the airport since multiple cancellations on Friday.

"It appears the storm has moved off overnight and the weather is looking quite clear now. It was pretty wild last night," she said.

Wild weather in the South Island affected a large number of flights at Queenstown, Invercargill and Dunedin airports with Air New Zealand offering customers the opportunity to transfer their bookings, or take credit.

Strong crosswinds were affecting flights at Queenstown on Friday, but Andrews said stormy weather in other parts of the country had affected travellers coming through Queenstown too.

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According to their schedule one flight had departed and another had landed, although two flights due from Christchurch at 8.30am were cancelled and delayed, and an outbound flight to Melbourne was also delayed.

Andrews said the airport's website was being consistently updated with information, but encouraged travelers to also check with their airline about whether their flights were affected.

It was possible there would be further disruptions on Saturday, although the weather was looking much clearer, Andrews said.

"There has been a bit of debris blown around the airport and the roads and surface flooding so we're just advising travellers to be careful," she said.

Two flights out of Invercargill were cancelled on Saturday, and one flight due to arrive from Wellington was cancelled, according to its airport's website.

An Air New Zealand spokeswoman said the weather conditions were changeable and there was "flow-on disruption" after Friday's weather.

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"We have not currently cancelled any services into or out of Queenstown, Dunedin or Christchurch this morning. Due to last night's weather conditions one service from Timaru and one from Invercargill was cancelled this morning," she said.