Heavy rain warnings have been lifted across Northland and Coromandel but the South Island is now of concern.
Heavy rain and wind that wreaked havoc in the north on Monday has moved south, and is expected to continue overnight through to late Wednesday morning, before beginning to ease.
Torrential rain is falling on the South Island's east coast, with flooding expected across Canterbury.
There are heavy rain watches and warnings in force for the Tasman District, Marlborough, Canterbury, North Otago and Dunedin.
Rivers are running high in areas already saturated by last week's heavy rain and flooding is likely in places, including the Ashburton District.
People in Otago have been urged to stay away from rapidly rising rivers and streams in the area and to prepare for high flows amid forecasts of up to 130mm of rain in North Otago and 90mms in Dunedin, Emergency Management Otago said.
Residents have also been reminded to keep away from low lying flood prone areas, particularly the Water of Leith, Lindsay Creek, Silver Stream and Henley sites.
Sandbags are available for those who need them from pick-up points in St Clair and Mosgiel.
Vulnerable parts of Otago will be under close watch on Tuesday night as heavy rain continues to fall, Emergency Management Otago said in an update.
Emergency Management Otago is asking people and residents in their homes to remain vigilant of water levels in their area overnight, particularly in areas more susceptible to flooding, as heavy rain continues.
More vulnerable areas include, but are not limited to SH1, which is likely to close north of Maheno at Kakanui river and north of Hampden at Big Kuri Creek due to flood waters; Mosgiel near the Silver Stream Spillway in Gordon Rd in particular; Henley township on the Taieri; Leith St, particularly between the foot and road bridges on the left bank of the Water of the Leith; Lindsay Creek, near the Hospice on North Rd; Milton, due to run-off from surrounding hills around Milton; SH1 at Waikouaiti; and parts of South Dunedin, such as around Bathgate Park.
In Christchurch, there is surface flooding around the Heathcote and Avon rivers. Eleven schools and five early childhood centres have closed due to flooding, while another preschool is shut due to road closures.
Christchurch has now officially set a new July rainfall record, according to MetService.
The station at Christchurch Airport has so far recorded 228mm of rainfall, beating the previous wettest July which saw 180.8mm of rainfall in 1977.
"It is also the first time since the station started recording that the monthly rainfall has exceeded 200mm making it the wettest month recorded there," MetService said.
There is also surface flooding on paddocks around Thompsons Track, an inland loop linking Rakaia, Methven and Ashburton.
There are a number of road closures, including State Highway 1 at Seddon in Marlborough.
In Dunedin, Portobello Rd is likely closed until tomorrow due to rockfall. The Dunedin Emergency Operations Centre has been activated as a precaution.
The Waitaki District and Dunedin City Councils have since activated their Emergency Operations Centres.
“We continue to monitor the rainfall across the region and watch for any impacts that this may have. The ground is really saturated following the last few weeks of wet weather and we may see slips, surface flooding by the end of the day," Emergency Management Otago group manager Matt Alley said.
More moisture will approach in from the north west as we move through the week, MetService meteorologist Lewis Ferris told RNZ's Morning Report.
Places that flooded last week are of concern today, he said.
Civil Defence Minister Kieran McAnulty said he had spoken to all the mayors in affected regions and they "all seem very relaxed".
"It’s either in control or being monitored, one isolated community down south but they’ve got all the gear they need," he said.
"Couple of closed roads in Timaru area but the mayor was quite happy."
"Most of the areas are as good as gold and those that are little bit worried, they know if they need help they’ll get it from NEMA (National Emergency Management Agency) but at this stage there has been no intervention at all."
Residents of the Mill Road Huts settlement near Pleasant Point, in Timaru, have been asked to evacuate by 5pm on Tuesday due to concerns around the integrity of the stop bank upstream from the community overnight, the local Civil Defence said.
Civil Defence Controller Jayson Ellis said the heavy rain has resulted in "significant surface water and localised flooding on many of our roads, which may not be signposted".
“While the weather has led to the closure of several roads and all fords in the district, the conditions are causing hazardous driving conditions throughout the district," Ellis said.
“Water on the roads can be deeper than it looks and may be hiding debris and washouts. We advise people to drive with extreme caution, avoid driving through flooded roads and if you can put off your trip, it would be safer to do so."
He also advised people living in rural areas in particular to avoid unnecessary travel and to "return home before dark as conditions will continue to deteriorate overnight".
Timaru residents in urban areas have been advised to continue to conserve water, as "the rain has caused a rise in turbidity at both the Pareora and Opihi intakes".
"While community efforts over the past few days have helped with storage levels, we need to continue this to ensure we can avoid having to put a boil water notice in place," he said.
Meanwhile, students living in around 20 low-lying flats close to the Water of Leith are being advised to prepare for a possible evacuation, the Dunedin City Council said.
Campus Watch are on Tuesday evening door knocking on homes located between Montgomery Avenue and Leith Street (Central), to warn residents of possible flooding if the stream overtops later on Tuesday night.
Students living in the affected homes have been advised to consider leaving immediately if they have somewhere else to stay, while those choosing to remain must have a bag packed and ready to leave at short notice.
The council said emergency services will evacuate remaining residents later on Tuesday night if necessary.
An evacuation centre will be open at Dunedin North Intermediate, and alternative accommodation options are available.
Some roads and rural fords are closed, and motorists have been advised to drive to the conditions.
The latest information on road closures in Dunedin can be found here.