There was a low to moderate chance of more tornadoes forming as thunderstorm warnings remained in place for Auckland and Northland.
Wind warnings were in place for parts of the lower South Island.
At least three waterspouts were seen over the Manukau Harbour and travelling towards shore when thunderstorms hit the Auckland region about 3pm yesterday.
Reports and images of the rare event - caused when the right combination of warm and cold air mixes over water - flooded social media.
Many weather watchers saw the spouts from Auckland Airport and Twitter user Joanne Bowley said "bit of excitement for a Tuesday arvo in Auckland".
Pictures sent to WeatherWatch clearly showed two funnel clouds reaching down towards the water beneath a grey sky.
While unable to say exactly how big they were, WeatherWatch head analyst Philip Duncan said they were large. "From what you can see on that photo one of them looks big, it looks ... like it would be much bigger than a boat, or a house maybe."
Water spouts - the name given to tornadoes over water - could cause winds averaging between 120-200km/h, Mr Duncan said.
"Out at sea they can look a lot more dramatic because they suck up all the water.
"We ... get these heavy thunderstorms coming through and it's good conditions for these things to form so it's not completely rare but to get these nice images we've seen today is quite special," Mr Law said.