Duncan said a large high in the South Island may help push the rain back out to sea today or tonight.
"However on Thursday the rain will be hovering just north of the North Island, possibly not clearing all of Northland or Coromandel Peninsula - then sliding back into the upper North Island across Thursday as the high and low pressure systems work together to create a wet nor'easter from Waikato and Bay of Plenty northwards."
"This rain could again become heavy and is worth monitoring - especially Coromandel Peninsula. However it may then clear yet again overnight for a time."
He said much of Northland and most Auckland escaped the worst of the overnight deluge, but those parts of Auckland and Coromandel Peninsula that were hit by floods had more than a month's worth of rain in the past 24 hours.
"These localised downpours are typical with a sub-tropical event like this."
Fresh thunderstorm warnings have been issued across the upper North Island.
MetService have updated the forecast with a severe thunderstorm watch issued for western Northland.
Thunderstorms are expected until 6pm and eastern Northland, Auckland, Coromandel and parts of the Waikato and Bay of Plenty are still under a watch until midday today.
He said more rain is expected for those regions on Friday, with heavy showers likely over the weekend.
Gisborne and East Cape are likely to get heavy rain too this weekend.
