Clark said winds overnight were going to be strong especially for Wellington and there would be rain as well.
The heaviest rain was expected in the west and north of the South Island. About the Westland ranges, rainfall could reach 280mm. The Tararua Range has now been added to this warning.
Motorists driving on Saturday night and during Sunday have been warned to take care or avoid travel as gale force winds could pull down trees and damage powerlines and lift unsecured structures.
People near rivers and streams were advised to use caution as the heavy rain will cause them to rise rapidly and may cause slips and surface flooding.
North to northwest winds were expected to strengthen, with gusts of 120 km/h possible in many locations from tonight.
Gusts may reach 140km/h around Fiordland, Wellington, Wairarapa and the Marlborough Sounds. The same warning was in place for areas in the north of the North Island.
Heavy swells and large waves were expected to affect western coasts on Sunday with coastal erosion in vulnerable areas making driving conditions hazardous about low-lying coastal roads.
"Basically it is not going to be a very nice week at all. It will be very unsettled," Clark said.