A number of severe wind and rain warnings and watches were expected to ease this morning.
But the wild weather returns later today when a second bout of wind and rain approaches the far south.
Flynn said gusts of up to to 133km/h have been recorded at Wellington's Mt Kaukau and 115km/h in Waiouru and Kaeo in Northland.
A huge amount of rain had also been recorded: 213mm fell on Mt Taranaki over the past 16 hours and 154mm in Arthurs Pass.
Despite the intense battering there were few emergency callouts.
Wellington Police said the worst appeared to be surface flooding around Mana Esplanade and reports of water washing into the Porirua boatsheds this morning.
Wellington police were asking motorists to take care on the morning commute because of surface flooding.
Roads in Paremata, Porirua and Mana required extra care because of flooding. Motorists were urged to slow down, drive to the conditions and watch their following distances.
Flynn said scattered rain was forecast for the South Island this afternoon ahead of another burst of gale-force winds and heavy rain.
"The main rain band will be east of the North Island by midday leaving a few showers around for both islands.
"Then later on today another front is approaching the south of the South Island."
She said the strong winds and rains would mainly affect the South Island high country.
That front would move up over the North Island tomorrow.