The deluge caused mayhem yesterday, blowing out manhole covers on some Wellington roads and cutting power to 130 Wellington Electricity customers.
A spokesman said all but one was reconnected by yesterday afternoon.
The Accident and Urgent Medical Centre in Adelaide Rd, Newtown, was forced to send several patients to Wellington Hospital when its back-up generator was affected by the flood, Radio New Zealand reported.
Cars in the medical centre's basement were partially submerged.
The Wellington Fire Service said crews responded to numerous flooding sites, with Newtown, Kilbirnie and Lyall Bay the worst affected.
Wellington City Council received more than 150 calls about flooding yesterday morning alone.
Strong gales also resulted in some Air New Zealand flights out of Wellington Airport being suspended.
On Browns Bay Rd on Auckland's North Shore, a truck and car collided at about 11am.
Meanwhile, Cantabrians were warned to avoid beaches and rivers after heavy rain put pressure on the region's sewage system.
Federated Farmers said the rain had managed to miss the farming areas most desperate for it.
Adverse-events spokeswoman Katie Milne said while the rain had broken the drought in most parts of the country, parts of the Central North Island had missed out.
"Farmers are gutted to see biblical quantities of rain falling while they are lucky to scrape up more than a few millimetres."
This week's weather
*Today and tomorrow - Fine weather predicted across the upper North Island.
*Thursday - Showers return to Waikato, Auckland and Northland.
*Friday - Cloudy periods expected.