MetService warns that the Wellington region is moving into another 24 hours, or more, of persistent rain - on top of already saturated grounds and swollen rivers.
Both Wellington and Wairarapa are under red heavy rain warnings.
Meteorologist Lewis Ferris told Checkpoint that rivers would be rising rapidly, and that there could be rain intensity of 25-40mmh in addition to what's already fallen.
Residents have been warned not to travel unless absolutely necessary.
Wellington Region Emergency Management Office regional manager Dan Neely told Checkpoint this evening the worst of the weather was expected tonight.
He says people should stay inside, avoid doing anything risky and report anything dangerous to 111.
This evening. Hutt Valley City Council said rising water levels were forcing evacuations in the suburb of Wainuiomata.
People at the northern end of Konini St, as well as Wetherby and Rata Sts, were being told to evacuate immediately.
The council said teams were going door to door but people in the affected streets should not to wait and should leave immediately.
Flights affected
The wild weather has caused at least 28 flights to be cancelled in and out of Wellington Airport, and all regional flights were cancelled this evening.
An airport spokesperson said the affected flights were both domestic and international.
He said it was likely there would be several more as bad weather intensified.
Earlier, residents in low-lying and flood-prone areas of the capital were being urged not to wait for official word to leave as torrential rain continued to cause slips and flooding.
The Wellington Region Emergency Management Office said people fearful of flooding at their house should act quickly and go elsewhere for the next 24 hours.
Heavy rain has pelted the region since Saturday but MetService is warning there is even more to come.
The forecaster this afternoon issued a rare red heavy rain warning for both Wellington and Wairarapa, lasting from 2pm Monday until 9pm Tuesday.
MetService says the forecast rain presents a threat to life from dangerous river conditions, significant flooding and slips.
A state of emergency has been declared for the Wellington region.
Man reported missing
Meanwhile, a search for a man missing in the Wellington suburb of Karori has been called off for the night.
The search was launched this morning after the man was reported unaccounted for.
Inspector Fleur de Bes said emergency services were contacted about 7.15am today by a concerned resident who had not been able to make contact with relative Philip Sutton.
Sutton's Karori South Road property was found to be hit by floodwaters and debris.
This evening, police advised the search had been called off, but would resume in the morning.
Emergency vehicles were out around the city early this morning, with pictures showing large amounts of water flowing along main roads, including along Adelaide Rd in Berhampore.
A police officer officer stationed south of the Basin Reserve said people were being evacuated from Berhampore as well as Ōwhiro Bay.
"It's bad, there's flooding everywhere."
Other areas badly affected include Kingston, where a major slip has cut off some residents, and Island Bay, where the suburb's main street is completely submerged.
Woolworths supermarket carpark nearby was also flooded and closed off.
The ambulance officer says residents in a couple of streets in Berhampore had to be evacuated, but no one was hurt.
RNZ's reporter at the scene said flooding around the Basin Reserve extended to John and Thompson Streets and all cars were being turned back. There were submerged cars down a side street. Three women standing on their doorstep said they were but were okay.
'Worst nightmare': Wellington resident wakes to landslide
A resident of the Wellington suburb of Brooklyn woke up to what he said was his "worst nightmare", as a landslide caused the wall of his bedroom to cave in.
CJ Kochar said he heard a loud noise around 5am, before the roof fell in and cracks appeared in the wall, which later broke.
He said it happened on the backside of the house, on Ōwhiro Road, so the front was unaffected.
Fire and Emergency was also there.
Kochar said he was fortunate that he had contents insurance, while his landlord had house insurance.
He said the raining in Wellington had slowed down "a little bit", but the entire street was flooded.
'Terrifying night'
An RNZ reporter in the Wellington suburb of Berhampore says residents have had a "terrifying night".
Ellen O'Dwyer is at Akatea St where residents have experienced flash flooding from heavy rainfall.
"At the moment, it's looking calm, but when you go into the properties - it's a starkly different scene."
Residents told her they had an "absolutely terrifying night".
O'Dwyer says flood waters around 3.45am rushed through the streets and pushed cars down the driveway and under garages.
She says firefighters were forced to axe elderly residents out of their homes and carry them on their backs through floodwaters to safety.
MetService's warning of severe thunderstorms said the thunderstorms were expected to lie near near Wellington, Karori, Makara, Khandallah, Ngaio, Miramar, Wellington Airport, Island Bay, Brooklyn and Hataitai at 05.37am.
The Transport Agency issued a warning about flooding on the section of State Highway 1 in the city from the Terrace Tunnel to the Basin Reserve.
Cook Strait ferry sailings have all been cancelled for the day and more are expected to be axed tomorrow.
Heavy rain and flooding in the weekend led to states of local emergency declared in the small town of Ōhura, Ruapehu District as well as the Whanganui District.
Multiple roads and highways were closed across the North Island due to flooding and slips.
On Sunday evening, an orange warning for heavy rain was in place for the Hutt Valley, wider Wellington Region south of Tawa, Wairarapa, Tararua ranges and southern Tararua District - for 31 hours from 11 am on Monday.
Parts of the South Island - in and around the Kaikōura Coast and ranges, as well as North Canterbury ranges east of Lake Sumner - could see nearly 130mm of rain between 10pm Sunday night and 11pm Monday.
Meteorologist Katie Lyons said a swirling low pressure system to the west of motu was tracking eastward across the country overnight.
"As that low - tonight and tomorrow - tracks eastwards, winds will flip around south-easterly and that's why we're seeing those eastern regions like Wairarapa and the Kaikōura coast under those heavy rain warnings.
"As those winds flip around we'll get rain continuing there as well as periods of heavy rain. Often when we get the combination of the longer lived rainfall with periods of heavy falls that's when we see those impacts," Lyons said.
