Wellington has been cut off and Hutt Valley residents have been told to prepare to evacuate their homes.
Police are now asking Wellingtonians to stay where they are now and avoid all non-essential travel.
State highways 1 and 2 have been closed, while Waiwhetu Stream breached its banks this morning.
Authorities fear parts of Kapiti may become isolated and St John ambulance has put more resources into the area.
A string of motorists is stranded on SH2 between Ngauranga and Petone where the road has been closed due to flooding.
Wellington motorist David Kyle is among those stuck in a vehicle.
He estimated floodwaters were about 30 to 40cm deep and between 500 metres and 1km in distance.
"The main barrier down the highway is blocking water from flowing down the hill across the northbound lane, into the southbound lane and out to the sea so it's just holding the water in a lake there."
There were vehicles parked up behind him as far as south as he could see.
In the Hutt Valley, the Wellington Region Emergency Management Office said people in the Waiwhetu Stream area should prepare to evacuate now.
"Place possessions up high if possible. Check on family and neighbours. If you feel uncomfortable evacuate now. Go to friends or family or higher ground."
Those with nowhere else to go could head to the Walter Nash Centre on Taine Street, Taita.
Hutt City Council is advising residents to check on family and neighbours and place their possessions up high if possible.
The riverbank car park is closed as a precaution. People can park in all metered car parks today for free.
Gracefield, Pukeatua, Waterloo and Normandale schools are closed. Eastbourne, Moera, Stokes Valley and War Memorial libraries, and the Naenae and Taita clubhouses are also closed.
All Hutt City kindergartens are now apparently closed. Parents have been asked to collect their children as soon as possible.
Residents should avoid unnecessary travel and stay away from waterways and drains.
The Porirua Emergency Operation Centre has been activated to deal with this morning's flooding and slips.
Parents with children at school are advised not to collect them early as authorities are expecting the rain to ease from 1pm.
The council is advising people to stay at home and not add to the traffic jams across the city and region.
Those who have been forced to leave their homes because of flooding have been asked to go to seek refuge with family or friends or the nearby North City Shopping Centre
The Porirua authorities are warning people to stay out of flood waters across the city as they are likely to be contaminated.
The council and contractors were having difficulty responding to flooding and slips on roads, reserves and private property.
Work was being hampered because of road closures, traffic jams and access difficulties.
SH58 from Paremata to Haywards Interchange at SH2, Greys Road and Paekakariki Hill Road are closed.
The highway between Mackays Crossing and Paremata is closed due to the severe flooding.
There is also severe flooding at Mana and the Plimmerton roundabout.
Eastern Hutt Road in Upper Hutt is closed to all traffic from the roundabout on Fergusson Drive to north of Reynolds Bach Drive. Re-directions are in place until further notice.
Due to flooding under the Silverstream Railway Bridge, the underpass has been closed to light vehicles.
Porirua Harbour will experience high tide around 11am and this may affect roads around Porirua Harbour and the Pauatahanui inlet. Motorists are asked to avoid the area if possible and take alternate routes.
There are numerous reports of surface flooding in Hutt Valley and police are responding to a number of weather related call outs.
The Hutt River is very high and has overflowed at some parts. Police recommend motorists avoid State Highway 2 between Upper Hutt and Petone due to surface flooding.
Motorists are asked to avoid non-essential travel. They should exercise caution, adjust their driving to the conditions, avoid any areas where there is surface flooding and be tolerant of other road users.
There are contractors in the worse affected areas who are managing traffic and motorists should follow their instructions.
Wellington City Council's regional emergency management said it was experiencing "a dynamic situation".
A Wellington-based student army has been announced in the wake of the natural disasters wreaking havoc across the capital.
Last night was marked by aftershocks, wind and rain - the motorway signs had replaced the tsunami warning to motorists with one warning of extreme weather.
This morning the official line is Wellington's CBD is open for business, but the city remains a bit of a ghost town.
The CBD has re-opened but several streets, including Featherston Street, are still closed because of the risk of falling glass.
This morning, there were few commuters on the street and very few suits on their way to work.
Inner city cafes which would usually be full of people having breakfast and queuing for coffee have empty tables.
Buses were running but have many empty seats.
The fuel that keeps Wellington running - coffee - is however still flowing for those who have ventured out.
One coffee outlet is offering free coffees to emergency services workers helping with the earthquakes and weather.
Wellington Mayor Justin Lester said many workplaces would now be ready to get back to work and described the forecast gales and rain as "nothing more than a gentle breeze" by Wellington standards.
Civil Defence has advised people to use commonsense when in the central city today.
Some buildings are still being assessed and areas, particularly around Featherston Street, are still cordoned off.
Police are controlling traffic on Featherston Street and making sure people stay away from damaged buildings.
Weni Ling's store Mama Sushi, on Customhouse Quay, is on the edge of one of the worst-hit parts of the city.
Her store was undamaged in the quake, but she is worried about further quakes.
"This building is very new so we're ok," she said. "I have been in New Zealand 16 years and this is the most awful [earthquake]."
"We are thinking of moving now, maybe to Auckland, somewhere with less earthquakes. Especially in the city, the business in Wellington cannot open.
"And we are just worried about the big earthquake. My kids are a little bit worried."
Alison Zikonda, who owns Monsignor Antiques in central Wellington, said the poor weather was "adding insult to injury" after the quake.
Her store was relatively unscathed. She had learned from previous quakes and fixed all of her shelves to the walls with steel braces.
"All of these valuable mirrors and things, and not one broke," she said. "So somebody's looking after me."
Zikonda says she is prepared for the "big one". She has blankets, duvets, food supplies and in her store, and has even attached a butcher's hook onto a rope "so if I'm stuck under furniture I can hook it onto something and pull myself out".
"I tell the neighbours to do the same but they never listen."
Due to severe flooding and slips the following roads are closed:
• SH58 from SH1 Paremata to Haywards Interchange at SH2
• Grays Road
• Paekakariki Hill Road
• SH2 between Ngauranga and Petone is closed northbound. Currently open southbound but congested and motorists should avoid travel on this route. There may be a short closure southbound to help alleviate flooding.
• SH1 between Mackays Crossing and Paremata - closed northbound and southbound.
• Miromiro Rd
• Udy St in Petone
• Harcourt Werry Dr between Taita Dr and Percy Cameron St
• Rain with heavy falls is expected to ease by midday today. In the 3 hours from 9am to midday, expect a further 20 to 30mm of rain on top of what has already fallen. Peak intensities of 10 to 15mm/hr.
• A heavy rain warning have been issued for Wellington, Kapiti and the Tararua Ranges.
• Grays and Paekakariki Hill Road in Porirua are closed, as well as State Highway 58 over the Haywards Hill.
• Mana College is closed due to flooding, but the exam room remains open.
• The CBD is open for business. Workers were being told to check with their employers whether their workplace was open.
• Passenger ferry services are back up and running but the port was still out of action.
• Wellington Railway Station has been cleared and trains and buses are back in action although the weather and power problems are causing some delays and there are restricted services to some places.
Tairua’s one-lane Pepe Stream bridge becomes a significant bottleneck every summer.