MetService says the weather on the West Coast is some of the worst they've seen.
Damage to a bridge near Te Taho and a large slip on the Fox Hills are being assessed.
The New Zealand Transport Agency expects some road closures to last for weeks as conditions worsen.
Meteorologist Andy Best says the weather is shocking.
"We've recorded close to 100,000 lightning strikes in the last 24 hours. I don't think we've seen that amount of strikes recorded before."
A state of emergency has been declared in Timaru, with the Rangitata River at risk of bursting its banks. State Highway 1 is shut, and the inland Route 72 - at the upper bridge - is also closed.
RNZ reports SH6 is closed from Hokitika to Makarora, with several slips blocking the road.
Timaru Civil Defence spokesperson Stephen Doran told Newshub the Rangitata River is at 10 times its usual volume and is spilling onto SH1.
"The river's in a mainly rural area, so we've been notifying farmers to move stock to higher ground."
He's urging freedom campers to pack up and move on, and warning residents of Rangitata should be prepared "to evacuate at short notice".
"Widespread flooding is likely. Please use extreme caution and ensure your own safety as the situation could change throughout the day."
Best says people will soon see heavy rain warnings for the lower North Island too.
"We also have a heavy rain watch for many North Island areas from Sunday through until Monday - parts of the Bay of Plenty, Taumarunui, Taupo, Taihape."
WeatherWatch said a mix of warm and cold air will "trigger some thunderstorms across the upper and western sides of the country over the next couple of days".