A cluster of businesses in the centre of Papakura are counting the costs of last night's thunderstorm, which caused "carnage" in a local arcade.

The dangerous storm swept across the city at rush hour, grounding flights, flooding homes and shops and leaving roads knee-deep in water.

Fire crews were called to 25 emergencies in the space of 45 minutes after the storm unleashed its worst over the South Auckland suburb.

Joseph Azouri, owner of Boodles restaurant, said his was the only business open in the Selwyn Centre when the thunderstorm started last night.

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A "river" of water ran through the Selwyn Arcade in Papakura last night. Photo / Supplied

"It happened real quick - all of a sudden there was just this downpour, and everything started to flood. Water started to come from one area, then all different areas," he said.

The water outside rose to knee-height and was pressing against the arcade doors, and covering his ankles inside the arcade.

"We literally had a river running through the mall."

Most of the water came off the roof but it also flooded down the stairs from an above-ground carpark and through a back alleyway.

"It was quite overwhelming. You just try and do the best you can and then stand back. When it's coming in at such a rate there's not much you can do."

In the law and accounting firm offices upstairs, water was pouring through ceilings and soaking walls, carpets and files before seeping into the shops below.

"You'd just block one area and double the amount would come in another area. I just started planning for the cleanup."

He called the fire service, which sent three crews from Papakura, Clevedon and Manurewa to help channel the water out.

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Azouri did not believe there was much structural damage to the building, but some shop owners would face a mess this morning.

Dozens of roads, businesses and houses flooded in Papakura. Azouri saw people standing outside in the dark or climbing on their roofs to check they were still sound.

Northern Fire and Emergency shift manager Paul Radden said most callouts were in Papakura dealing with properties flooding, roofs leaking and inundated roads.

At one property people needed to be rescued by firefighters after becoming trapped by rising floodwaters.

"There was one property where the people couldn't leave their property due to flooding but they weren't in danger," said Radden.

Flights in and out of Auckland airport were disrupted during the storm. All planes were temporarily grounded and six flights diverted.