More rain is forecast for an already deluged Coromandel with highways down to one lane and motorists warned to take care in the treacherous conditions.
The MetService has now issued a warning for the region with heavy downpours expected to fall until tomorrow morning.
Authorities are now closely monitoring this afternoon's high tide with fears it could cause flash flooding and block roads for a second time today.
The flooding has forced a Coromandel school to close for the day.
The Waikato Civil Defence says Manaia School will shut early at 12.30pm due to flooding.
The school is on the western side of the Coromandel Peninsula.
Civil Defence also says a slip has closed Kennedy Bay Hill near the Devil's Elbow.
Residents of Whitianga awoke to find themselves isolated from the rest of the region as flooding across the highway blocked the main roads in and out of the eastern township.
The Zealand Transport Agency closed State Highway 25 to the north and south of Whitianga but reopened one lane to traffic mid-morning.
There was also a report of a slip on the road at Kuaotunu hill.
NZTA and Thames-Coromandel District Council contractors were checking the extent of flooding throughout the region.
Civil Defence described conditions in the region as "pretty wet and grotty" and encouraged those venturing out on roads to "drive like a nana".
There have been few reports of damage with the Fire Service coming to the aid just one homeowner with a flooded garage.
The Thames-Coromandel District Council said it was now low tide which was good news for the region's usual flooding hotspots but were on alert with high tide expected at 3pm.
MetService is warning another 80 to 120 mm could fall in the next 24 hours on top of what has already fallen.
In some places, hourly rainfall rates in excess of 30mm per hour were likely.
It said the slow-moving trough would not clear the area until early Friday morning.
The forecaster has also issued a severe weather watch for the neighbouring western Bay of Plenty and eastern Waikato for today and tomorrow morning. It says these regions may experience localised heavy rain.
A severe weather watch has also been issued for prolonged heavy rain covering the west coast of the South Island this weekend.
But forecaster Weatherwatch.co.nz says the heaviest rain has now eased around Whitianga and surrounding areas with sunny spells likely in the rain-drenched eastern Coromandel this afternoon.
Head analyst Philip Duncan said while there would still be some patchy rain, with the chance of an isolated heavy falls it would improve this afternoon.
While the rain was intense it was not widespread beyond the Coromandel region.
Mr Duncan advised local residents to monitor the rain radar at MetService as well as the latest roading information from NZTA.
Mixed weather around NZ
It's dawned a tale of two islands today with northern New Zealand sitting a whopping 20 degrees higher than cities in the south.
WeatherWatch head analyst Philip Duncan said a warm, humid night in Auckland has kept temperatures up at 18C while Dunedin is shivering on -2C.
"New Zealand is divided into three pieces at the moment. Cold in the south. Cloudy and damp through middle New Zealand and warm and humid with tropical downpours in the north" Mr Duncan said.
At 8am Auckland had 18C with a mix of sun and cloud.
But at the other end of the country Dunedin was experiencing frosty conditions and sitting on a nippy -2C.
Weather around NZ
• Auckland: Showers, some heavy, light northeasterly winds. High of 23
• Wellington: Cloudy with southeasterlies. High of 16
• Christchurch: Cloudy with fine breaks this afternoon and light northeasterlies. High of 15
• Dunedin: Fine and light northeasterlies. High of 16.