Dairy prices have proven to be highly sensitive to New Zealand's weather.
In February, prices spiked higher when drought conditions in parts of the country looked like they would have an impact on production. When that proved not to be the case, prices slumped.
Parts of the country, particularly in the east, have remained drier than normal following drought conditions early this year.
Primary Industries Minister Nathan Guy said the ministry would keep a close eye on weather conditions in Northland and the rest of the country.
"An El Nino increases the likelihood of more frequent or severe adverse events, but only accounts for part of the variance in New Zealand's weather," he said.
Guy said the impacts of an El Nino were typically less severe and less predictable than in Australia. However, he said it was important farmers prepared for the increased chance of adverse events.
El Nino is a major global climate fluctuation that occurs at the time of an ocean warming event. For New Zealand, it generally leads to stronger or more frequent winds from the west in summer, leading to drought in east coast areas and more rain in the west.
In winter, the winds tend to be more from the south, bringing colder conditions. In spring and autumn southwesterly winds are more common.
Niwa said indications were that El Nino was certain to continue over the next three months and was "extremely likely" to persist over summer.
"The current state of the ocean-atmosphere in the Pacific and the international consensus forecast suggest that this event could then rank among the four strongest El Nino events recorded," it said.
For September-November, above normal pressure is forecast over and to the south of Australia, while below normal pressure is expected to the east of New Zealand.
September-November 2015 rainfall totals were most likely to be in the below normal range for the north and east of the North Island, it said.
Seasonal rainfall totals were likely to be near normal or below normal in the west of the North Island and the north and east of the South Island.
September-November 2015 soil moisture levels and river flows were most likely to be below normal in the north and east of the North Island and the east of the South Island.
In the western regions of both Islands, soil moisture levels and river flows are likely to be in the near normal or below normal range.
El Nino
• A natural feature of the global climate system.
• Occurs at the time of an ocean warming event.
• Leads to stronger or more frequent winds from the west in summer.
• Typically leads to drought in east coast areas and more rain in the west.