Farmers in the western, wetter parts of the country often face significant damage to pastures from too much rainfall, and it is also harder for stock to thrive in the constant wet.
Those in the east, with dry conditions, need to consider food availability for stock.
Niwa forecaster Chris Brandolino said it remained to be seen what form El Nino would take, but there was concern it could make things tougher for farmers in eastern parts of the North and South Islands that were parched from last summer.
"Those farmers really depend on normal rainfall for their way of life and they endured a really rough summer. As we head into summer again, El Nino can make things even worse."
The last big El Nino, in the summer of 1997/1998, cost the country hundreds of millions of dollars.
Federated Farmers' adverse events spokeswoman, Katie Milne, urged newly established farmers to take advice from long-time locals on what an El Nino would mean for their district.
El Nino was already a strong talking point in the rural sector, she said, and concern had grown with recent international forecasts.
"Forget about hoping it's going away - it's not going away - so it's really time for farmers to put some plans in action and set some goals."
Meanwhile, Niwa reported that temperatures over the next three months were likely to be average or below average in all regions.
Rainfall totals were likely to be in the near normal or below normal range for all regions except for the west of the South Island, where the chances of near normal or above normal rainfall were equally likely.
What is El Nino?
• El Nino is a climate pattern associated with unusually warm ocean waters in parts of the Pacific Ocean.
• An El Nino event can have a significant impact on weather patterns, ocean conditions and fisheries across a large part of the Earth.
• During El Nino, cyclone conditions in the tropical South Pacific shift eastwards, causing more cyclones than normal in areas like the Cook Islands and French Polynesia.
• El Nino can also cause heavy rainfall and flooding over Peru, and droughts over Indonesia and Australia.
• In New Zealand, an El Nino event could make western areas wetter, and the eastern seaboard drier than usual.
• El Nino means the little boy or Christ child in Spanish. It was first observed in the 1600s by fishermen off the South American coast.