"There was a mini tornado heading our way," tweeted Merryn. "There was a big ominious bit of sky above my head, so naturally that was the fastest I've ever walked home."
Weatherwatch.co.nz forecaster Philip Duncan said the cloud was a water spout, not a tornado.
He said it had the potential to flip yachts and small boats.
People in Auckland Harbour, Devonport and the eastern bays should be "vigilant" as the spout was heading east , he said.
"Waterspouts are generally fairly safe to watch from land but should it move towards land people should immediately take cover indoors away from windows."
Mr Duncan said the conditions creating the water spout were similar to those that at the time of the deadly Albany tornado last year.
"Big cloud build ups can create wild air currents and in turn they can create localised funnel clouds - which can lead to small waterspouts over water or small tornadoes over land."
Mr Duncan said there was a low risk of small tornadoes or more waterspouts forming in the next two days.
Having a water spout form so close to the city centre was a rare sight, he said.
"It's common to get waterspouts in New Zealand but certainly rare to see such a clearly defined one right in the CBD of Auckland Harbour".