About 375 homes in Wairarapa remain without power and several roads around the capital are affected by landslips, erosion and surface flooding, and motorists are advised to take care.
Air New Zealand chief executive Greg Foran said the schedule was packed due to the school holidays.
Winter illnesses including Covid have also meant that Air New Zealand's absenteeism rate is about three times higher than normal, he said.
Flights only resumed in and out Wellington this morning, with one flight leaving early this morning and a number were scheduled from about 8am onwards, he said.
Asked when passengers who had their flights cancelled yesterday could expect to be rebooked, Foran said it was a challenge, partly because it was one of the busiest parts of the school holidays as people looked to return home.
"It's obviously pretty full for today, Saturday and Sunday and we've got to get planes and crew repositioned.
"So that's why I just want to be clear with people, we'll certainly do our best to get as many people moved today as we can, but the reality is we'll still be moving people Saturday and in some cases Sunday."
Air New Zealand will also be looking at the possibility of buses and Foran encouraged anyone who did not have to travel to look at not flying and putting their fare into credit.
Non-refundable tickets would be put into credit, but people with a refundable ticket would be able to get refunded, Foran said.
Air New Zealand has provided accommodation in most cases but hotel rooms were not always available and Foran said he was feeling for those with no alternative way to get home.
"I am aware that there are some cases in some airports where some people have ended up having to stay overnight, but in most cases ... we do get people accommodation."
The wild weather displaced aircraft and crew which would affect flights across the country and it may take several days to get passengers to their destinations, Air New Zealand said.
Cook Strait ferry sailings were cancelled, with the Interislander rebooking 600 affected passengers on new sailings.
Interislander ferries were sailing again, with the Kaitaki leaving Picton about 2.50am and due to arrive in the capital after 6am.
At least 1000 homes north of Wellington remained without power, in the Kaitoke area north of Upper Hutt, and also in Wairarapa.
Wellington Electricity said equipment had been damaged and it is working to restore power to affected customers as quickly as possible.
Several roads around the capital are affected by landslips, erosion and surface flooding, and motorists are advised to take care.
Respite ahead, but forecasters predict it won't last long
It's been a week of extremes across the country thanks to a mixed bag of weather, with some areas being hit particularly hard. However, there might be some respite before New Zealand is hit again.
Wild weather battered parts of the country yesterday, cancelling flights and ferry services and closing roads.
Once we get through this cold southerly flow currently making its way across New Zealand, we will see a ridge of high pressure spread over the rest of the country.
This means a lot finer weather around the country for people travelling home after the school holidays, apart from some residual showers in the east of the country.
"While most Kiwis can still expect cloudy conditions, the windy, sodden conditions of the week gone by will be somewhat more of a memory - making for a nice last weekend of the school holidays," MetService meteorologist Tui McInnes said.
This respite is much needed for areas like Wellington after the city has been hammered by wild weather. Wind and rain have caused road closures and power outages, and brought large swells of up to 10 meters to coastal areas.
It ripped the roof off a Lower Hutt cafe and left Wellington Airport packed with travellers dealing with cancelled bookings.
Unfortunately, forecasters predict that this respite won't last very long.
A low-pressure system is developing off the coast of Queensland and tracking towards New Zealand currently.
It will hit Northland first on Sunday, bringing heavy rain and severe gales to the area.
As the low-pressure system is originating from the tropics, it is also expected to bring some overnight high temperatures for Northland. MetService estimated it might get as high as 13C on Sunday night with a broad region of humidity and strong east to northeast winds.
MetService also said that the tropical low-pressure systems are headstrong and unpredictable.
On Monday, it is forecast to spread down the country and hit Auckland, the Coromandel, the western Bay of Plenty and northern Waikato and is forecast for the development of both significant heavy rain and east to northeast severe gale winds.
On Tuesday, the band of rain and strong winds will continue to move slowly south over northern New Zealand and MetService predicted that Auckland, the Coromandel, the western Bay of Plenty and northern Waikato will again have significant heavy rain and east to northeast severe gale winds.
State Highway 2 has reopened to two lanes at the site of today's slips in the Waioeka Gorge between Ōpōtiki and Gisborne after the road was opened to one lane yesterday afternoon.
Waka Kotahi NZTA National Emergency Response Manager Mark Owen said getting SH2 reopened was a priority with SH35 closed between Ōpōtiki and Te Kaha after a section of the eastbound lane near Motu River bridge collapsed into the river last night.
"SH2 through the Waioeka Gorge is an alternative to SH35 for vehicles (excluding over-dimension vehicles) travelling between Ōpōtiki and Gisborne, but we advise people to take care. While the road has reopened to two lanes at the site of today's slips, traffic is still reduced to a single lane on the southern approach to Motu Bridge, 7km west of Matawai, due to an earlier underslip."
Owen said the agency knew how important these connections were to communities on the East Coast – to access necessary services, such as food and healthcare, to get kids to school, to run businesses and to stay in touch with friends and whānau.
"With the rain easing, our contractors are working incredibly hard to make the most of the relatively settled weather forecast over the next four days.
"There is a lot of work to be done. The river is still incredibly high and the road is still moving," he said.
Contractors and geotechnical specialists are working to ensure the safety of the site, as well as undertaking investigations into options for solutions.
Owen encouraged everyone to take care, allow additional time for their journeys and be patient, especially with other road users and road workers.
"Safety is our single biggest priority and we will not reopen the road until we are confident it is safe to do so, for both road users and our road workers, but I want to assure everyone our teams are working extremely hard to see that happen as soon as possible," he said.
- with RNZ
