WeatherWatch head analyst Philip Duncan estimated the waterspout was at least half a kilometre tall and 50m wide, with wind speeds up to 120 km/h.
He said the unstable conditions, perfect for creating the spinning winds, were similar to those which caused a tornado that tore through the North Shore last May, killing a construction worker at Albany.
"Big cloud buildups 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."
David Simonaire, who took the dramatic photograph at left, was in the Sky Tower with his wife Corrine. The couple, from Maryland in the United States, are here on holiday.
"We just came around the corner on the viewing deck and there it was - it was pretty incredible," Mr Simonaire said last night. "I've never seen anything quite like it. "
Boaties in the path of the harbour spouts were advised to head to land.
Mr Duncan said the air mass that caused the twisting winds would remain over the North Island today, with the prospect of downpours in Northland and the Waikato.
"These afternoon and evening showers may have torrential rainfall rates which can see drains and creeks turn into raging torrents in minutes," he warned.
Deadly tornadoes
* In May last year a tornado struck Auckland's North Shore, killing Benedict Dacayan, 37.
* In August 2004, Rosina Dawn Wikohika, 55, of Levin and her grandson Gary Mason, 10, were killed with a tornado struck the Taranaki town of Motunui, north of Waitara.
* On August 25, 1948, a major tornado hit the Hamilton suburb of Frankton, killing three people and damaging or destroying dozens of houses.
New Zealand's large tornadoes since 2005
* June 2011 Taranaki tornadoes $1.6 million in estimated insurance claims
* May 2011 Auckland tornado $6 million est.
* July 2009 Kaitaia tornado $7500 est.
* July 2009 Taranaki tornado $500,000 est.
* Oct 2008 Cambridge tornado $1 million est.
* July 2007 series of tornadoes $8.3 million est.
* March 2005 Greymouth tornado $9.2 million est.
Source: Insurance Council of New Zeland
http://www.icnz.org.nz/current/weather/