MetService is warning of thunderstorms and heavy rainfall in many parts of the country, and the risk of "large, damaging hail and possibly a small tornado" in eastern parts of the North Island.
Many roads are closed today due to flooding in Otago and Southland, where some campers remain stranded.
MetService has issued a severe thunderstorm watch for most of the North Island, from Northland down to Wairarapa, and for several areas in the South Island, including north and central Otago, Dunedin, Clutha and Southland.
The weather authority said in a statement there was a risk thunderstorms may become severe, resulting in surface and/or flash flooding.
It said there was a "moderate risk of large damaging hail and possibly a small tornado" in the far eastern parts of Taupō, Taihape, Hawke's Bay and the Tararua District.
There was also a risk of large hail in eastern Otago, and possibly hail larger than 20mm in diameter in South Canterbury.
About 200 festival goers are stranded at a camping ground in Otago with the main road out flooded.
It is the last day of the five-day-long Whare Flat Folk festival but people might have to stay at the Waiora Scout Camp for another night.
Festivals promotions manager Annabel Roy said there is plenty of food and everyone is safe and keeping themselves well entertained.
Southland District Mayor Gary Tong said while the region had been spared major damage Waikaia locals were looking after several campers who had to be evacuated.
"They certainly can't get out of Waikaia yet, but I understand the river is receding rather quickly, so hopefully people will be able to return to their normal life by the end of the day as long as the rain keeps away."
A helicopter would fly over the area affected by floods today, to search for any stranded campers remaining in the Waikaia valley.
Another severe thunderstorm warning had been issued for the area this afternoon.
Otago's Waitaki district was hit especially hard by the flooding, with the Otematata River overflowing its banks, after a hasty evacuation of campers there. But there had been heavy local downpours across much of the South Island as well as Northland, the Coromandel Peninsula, eastern Waikato and Taupō.
Risk water system may become contaminated
Boil water notices were in place for many places in Otago due to the flooding, especially for those using a bore water supply, and people should check for updates about water warnings on their local council website before using tap water.
Dunedin City Council said the waste water system may have been affected by heavy rain, so the flood waters should be treated as contaminated.
RNZ reporter Sarah Robson is in the Otago town Middlemarch and says many of the town's roads remain closed, some with knee-deep flood water, and others covered in mud and silt.
The council is asking Middlemarch residents not to flush their toilets until further notice after a lightning strike cut power to the area. The power cut means the town's sewerage system won't operate as usual, and there's a risk wastewater flooding will occur. Power is expected to be restored about 4.30pm today.
From midday, a tanker would provide water to residents wanting to fill up containers beside the Strath-Taieri Community Centre.
Many roads closed in Otago, Southland
The Transport Agency has closed sections of State Highways 83, 87 and 90 due to flooding, with various detours in place.
Many local roads were affected, and in Otago, there were still closures on State Highway 87 between Kyeburn and Outram, and between Otematata and Aviemore due to flooding and a washout; as well as on State Highway 90 between Waikoikoi and Tapanui.
In the Bay of Plenty, State Highway 2 was also closed between Nukuhou and Kutarere, and between Opotiki and Gisborne, because of flooding and slips after heavy rain last night.
MetService said 150mm of rain had fallen on some parts of Otago in the last 24 hours, with one weather station in the hills recording more than 200mm between midday on 1 January and midnight last night.
Otago Civil Defence controller Matt Alley said motorists should be particularly careful on the roads today, and should highwaycheck conditions before heading out, as well as the state of local roads, which were posted on local council websites.
Thunderstorms could take place this afternoon that might bring localised downpours and flash flooding, which could be severe from Clutha to North Otago, with Dunedin within the area that could be worst hit.