Heavy rain watches have been issued for parts of the South Island.
They cover the Westland District ranges, the Buller district, Tasman north-west of Motueka, the Nelson Lakes, the Bryant Range and the Rai Valley, as well as the ranges of Marlborough north-west of the inland Kaikoura Range.
Niwa principal scientist Chris Brandolino said Buller and Tasman could get a month's worth of rain in 48 hours.
"Many areas probably in these regions seeing a couple of hundred millimetres or more of rain over 48 hours, so yeah this'll be some pretty beefy rain for that region."
The rain would then move up over the North Island, he said.
Meanwhile, MetService meteorologist Mmathapelo Makgabutlane said an atmospheric river was expected to bring heavy rain and strong winds in coming days, starting in the South Island and moving north.
She said it was difficult to predict how much rain would fall.
"The main message is that we are expecting quite a lot of rainfall coming in the coming days."
Initially the heavy rain was forecast for the west and the top of the South Island including Nelson, Tasman, parts of Marlborough, towards Buller and down the West Coast of the South Island, she said.
But from Thursday into Friday the rain would head to the North Island and once again it was forecast for the northern and western regions, she said.
An atmospheric river was forecast.
"In the atmosphere we've got these columns of air and moisture - and what we're seeing now is this long column of moisture heading down towards Aotearoa and with that moisture it really fuels the weather systems that we're seeing.
"So the actual weather system that we'll be experiencing is a low pressure system but that atmospheric river really just gives it that extra moisture and juice that it needs to bring the heavy rain that we'll be seeing."
Whenever there were watches or warnings in place there was always the possibility of flooding and slips, she said.
MetService warns people in those areas to ensure their drains and gutters are clear to prepare for heavy rain.
People should avoid low-lying areas and drive cautiously, it advises.
MetService says the watches are likely to be upgraded to warnings on Wednesday morning, for everywhere except the Nelson Lakes.
