"We'll transition away from El Nino into neutral as we go through autumn and early winter," Duncan said.
"By the time we reach spring, we may be heading towards La Nina."
Niwa scientist Chris Brandolino said the outlook for winter was for above-average temperatures but average or below average rainfall.
"The next three months are going to be warmer but that isn't to say there aren't going to be cold snaps or frosts," Brandolino said.
Duncan said it was likely there would be more westerlies for the South Island, which meant the wet weather the west coast has been having will continue and Canterbury's drought may not end.
"We can have anything thrown at us because we are two islands in the Roaring Forties," Duncan said.