The country is waking up to the chilliest start of the year after many towns in the South Island froze through the night.

Air direct from Antarctica has sent overnight temperatures plunging from Kaitaia to Invercargill with everywhere recording low, single-digit figures.

Auckland has endured its coldest night since last spring dropping to a nippy 6C and some suburbs dropped to an even cooler 4C.

Parts of the capital have hovered just above zero, and Upper Hutt recorded 2C. The central city was slightly warmer on 6C.

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The morning frost has also caused problems for the city's trains. There are delays and cancellations on the Johnsonville line because the track is slippery.

But in the deep south temperatures are incredibly cold. Alexandra hit a hand-numbing -2.7C and the MetService warned it would actually feel like -5C.

Christchurch has also dipped below zero for a frosty start to what promises to become a blue-sky day.

The icy blast follows blustery weather that hit the country yesterday and today, bringing down trees in the capital, as well as delaying public transport.

Although most of the country's main centres will be shaking off the icicles this morning, the sun should be out in many places, MetService meteorologist Sarah Haddon said.

The sun would be short-lived though: Even colder weather is expected to roll in this week.

Overnight the clouds were expected to clear, which is what brings the temperature down, Haddon said.

"Cloud cover inhibits some of the cooling, the clear skies overnight is the thing that really brings the temperature down."

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Despite the clear skies, some "quite strong northwesterly winds" will bowl through many places.

"That will be something to watch out for."

A fresh weather watch has been issued for northwest gales over the South Island today and the possibility of destructive gales in Fiordland, Southland, Otago and parts of Canterbury.

Earlier weather chaos this week forced a Cook Strait ferry to take a seven-hour journey to avoid rough seas.

The Bluebridge ferry tried to dodge the worst of the wild weather on Sunday night, which saw 4-metre swells and southerly winds tipping just under 100km/h whip through the passage.

Strait Shipping spokesman Ed Menzies said to make the trip more comfortable for passengers the ship's master took a more southbound course and slowed the vessel, which avoided the worst of the swell but meant the journey took seven hours.

The crossing normally takes about three hours.

Wellington roads were affected by flooding and a passenger train struck a tree that had fallen on the tracks after wild weather left a trail of havoc across the lower North Island.

The Wellington to Johnsonville journey was delayed after a commuter train hit a tree.

All train services on the Melling line were cancelled after strong winds damaged barriers between Petone and Wellington.