The National Institute of Water and Atmospheric Research (NIWA) has declared the official arrival of El Niño.
The weather pattern - which usually causes dryness in the east and more rain in the west - is likely to continue over summer, NIWA said.
It said the country will see dramatic temperature swings over the next three months, with periods of unseasonable warmth followed by sharp cold southerlies.
The north and east of the North Island could experience below normal rainfall while the west of the South Island was most likely to see above normal rainfall.
There would also be stronger than usual winds, with the pressure pattern delivering more westerly winds that would likely lead to some prolonged dry spells to the north and east of both islands, NIWA said.
It said strong fronts will occasionally impact the western and lower South Island, delivering heavy rainfall and a risk for flooding
Rainfall is most likely to be below normal in the north and east of the North Island and above
normal in the west of the South Island.
The fire risk will be higher than last year for some areas, but marine heatwaves were expected to be less persistent and widespread.
There was around a 100 percent chance of El Niño continuing during October-December and over 95 percent chance it will persist through summer, NIWA said.
