Cars in the medical centre's basement were partially submerged during the rain.
The Wellington Fire Service said crews responded to multiple flooding incidents in the inner city, with Newtown, Kilbirnie and Lyall Bay the worst affected.
Wellington City Council received more than 150 calls about flooding this morning. The council advised motorists to use extreme caution and avoid driving until the heavy rain eased.
Strong gales also resulted in some Air New Zealand flights out of Wellington Airport to be suspended.
Meanwhile, Cantabrians were warned by health authorities to avoid beaches and rivers after heavy rain put pressure on the region's sewerage system.
Christchurch City Council said sewage overflow discharges had gone into the Avon/Otakaro River, Heathcote/Opawaho River and Akaroa Harbour.
Canterbury Medical Officer of Health Dr Alistair Humphrey said water quality in the Avon and Heathcote Rivers rarely met recreational water standards, but at the moment both rivers were particularly contaminated and contact with the waterways should be avoided.
"People should in general avoid rivers and the beaches for at least two days after any significant rainfall event, not only this one. This means it's not safe to drink water from rivers or use the rivers or estuary for recreational use," he said.
Forecasters say the weather is set to calm down by tomorrow.
MetService forecaster Elke Lowe said showers would linger in Wellington, Wairarapa, Hawkes Bay, Gisborne and the south of the South Island until tomorrow evening.
"But for most parts of the North Island it should be generally fine conditions."
And WeatherWatch.co.nz weather analyst Philip Duncan said the rest of the week should be dry, but with some frosts in the central South Island.
"Rain develops again for Northland on Wednesday afternoon, maybe northern Auckland by the evening and stays the same on Thursday as well.
"And another front comes up the South Island on Friday."
Federated Farmers said the rain had managed to miss the farming areas most desperate for rain.
Adverse events spokeswoman Katie Milne said while the rain had broken the drought in most parts of the country, the exceptions were the areas which had been affected the longest.
"Farmers are gutted to see biblical quantities of rain falling while they are lucky to scrape up more than a few millimetres.
While much of Rotorua got a good soaking, drought-stricken Reporoa remained dry.
Parts of Gisborne city were now out of the woods, but the driest areas of the region were lucky to get 6mm of rain.
FORECAST
Today: Frequent squally showers in morning then clearing by evening.
Tomorrow: Fine, cloudy periods with cool southerlies.
Wednesday: Showers and cloud increasing.
Thursday: Showers and cloud.
- NZ Herald with nzherald.co.nz and Newstalk ZB
