Civil defence authorities advised people in low-lying areas on the North Island's Coromandel Peninsula to evacuate to higher ground.
Air New Zealand suspended flights from Tauranga Airport and the military placed 500 troops on standby.
The storm appeared to be skirting the main city of Auckland, where authorities had earlier worried it could cause major problems. Authorities were advising people in Auckland to avoid traveling out of the city if they could avoid it.
The MetService weather agency predicted rainfall could exceed 100 millimeters in some places and cause more flooding in areas still recovering from heavy rainfall last week.
Last Thursday the town of Edgecumbe was flooded when a river burst through a concrete levee on the Rangitaiki River as the remnants of Cyclone Debbie hit. The water forced 2,000 people to evacuate and flooded hundreds of homes.
Many people have been unable to return to their homes since then and authorities have been scrambling to shore up the breached levee. The system will be tested again by the latest storm.
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