MetService severe weather forecaster Eric Brenstrum said about 100mm of rain fell in parts of the Canterbury Plains overnight, and a bit more than that in Banks Peninsula.
The heavy rain was expected to continue in the region today but would probably clear tomorrow.
A MetService severe weather warning remains in place for Canterbury and Otago.
In the Far North, firefighters have had to deal with the aftermath of a suspected tornado overnight.
Fire Service northern communications centre shift manager Jaron Phillips said at 9.45pm emergency services received reports of a tornado near Taipa, about 40km north-east of Kaitaia.
"Apparently five trees were knocked down - one very large tree - and were completely blocking State Highway 10."
Firefighters and roading contractors used chainsaws and a digger to remove the trees.
The road has since reopened.
Mr Brenstrum said there was a burst of heavy rain and thunderstorms in the area last night, which would be consistent with a tornado.
Snow is also effecting roads in the upper South Island.