NIWA fears this year's El Nino may be as bad as 18 years ago, when widespread drought cost the country a billion dollars in lost exports.
International guidelines indicated a 97 percent chance of El Niño continuing over the next three months and a 90 per cent chance it will continue over summer.
El Niño typically sees the west of New Zealand wet, and the east very dry.
Niwa forecaster Chris Brandolino said it was looking like it could be as significant as the El Nino in the nineties.
"There are some indications it could be a very strong El Nino, it could rival the 97/98 one. It is probably premature to say that for sure, but some of the ingredients for that are in place. That is mainly the unusually warm water temperatures east of the date line.
"That is the fuel which sets off a chain reaction starting with more rainfall. That has a domino effect, which could have consequences for New Zealand.
"A strong El Nino doesn't always mean strong impacts.
"In other parts of the world, there is a connection between strong El Nino and strong impacts: in New Zealand we can have strong impacts during a strong or weak El Nino."