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Niwa National Climate Centre forecasting principal scientist Chris Brandolino said residents could expect unsettled weather with "sharp cold snaps" from September to November.
"The central Pacific El Nino event that arrived in March this year has ended, giving way to El Nino Southern Oscillation (ENSO) neutral conditions, owing to cooling sea surface temperatures in the tropical Pacific and a neutral Southern Oscillation Index during August."
He said the oceanic ENSO neutral conditions were likely to continue over the next three months.
"An area of warmer than average seas in the west-central tropical Pacific is expected to occasionally influence New Zealand's weather patterns, contributing to sub-tropical low pressure systems that can bring heavy rainfall.
"For September to November, air pressure is forecast to be lower than normal in, and particularly south of, the New Zealand region.
"This is forecast to bring more southwest quarter winds than normal for the season as a whole, although periodic easterly quarter winds are probable.
"September and at least the start of October are forecast to be particularly unsettled, along with an elevated risk of sharp cold snaps.
"Those with interests in New Zealand's primary sectors, like agriculture, should pay close attention to weather forecasts to assist with mitigating potential impacts."
In inland Otago and Southland, temperatures are "about equally likely" to be near average or below average, and rainfall totals, soil moisture levels and river flows are likely to be near normal, he said.
In coastal Otago, temperatures are likely to be near average, rainfall totals are "about equally likely" to be near normal or above normal, and soil moisture levels and river flows are most likely to be near normal.