Civil defence officials in Whanganui says they are bracing for a long recovery, with the true extent of the damage still unknown.
More than 400 people have been directly affected by the city's worst recorded flood.
Civil Defence said at least 30 roads, both rural and urban, were closed, with contractors continuing to work to clear a large number of fallen trees and slips.
The city bridge remains open, but Whanganui east is cut off and can only be accessed by a 40-minute detour.
Rural roads near Whanganui could be closed for a month or more, while drinking water is being brought in to a small communtity in South Taranaki.
Mayor Annette Main said the flooding was a nightmare and some roads around the city could be closed for more than a month. The army is still deployed.
"Our rural roads are still closed. We received updates that some of them may be closed for a month or more.
"We may have to look at some of the people in those areas and what we can do about getting some of those people out," she said.
"I've just spoken with a man whose mother lives in the Anzac Parade area and she wasn't able to get insurance so she's lost everything with two metres of water through her house", said Ms Main.
"While it's disastrous for us as a community, individually for people it's just a nightmare, a nightmare," she said.
Whanganui flooding Photo: Claire Bullock
Ms Main said the Whanganui East community is still completely isolated.
Areas are under water following widespread flooding, which has also affected parts of Manawatu and Taranaki.
Civil Defence Minister Nikki Kaye has been looking at the damage in Whanganui and Waitotara today.
She said the scale of the flooding was very severe.
"In these situations central government is here to assist, we do pay for a range of things and we'll be working that through with the relevant authorities, but our thoughts are with the families tonight who are not in their homes."
Civil Defence Minister Nikki Kaye and Whanganui Mayor Annette Main by the still very swollen Whanganui River. Photo: RNZ / Carla Penman
The Civil Defence Ministry said states of emergency remain in place for Whanganui, Rangitikei and Taranaki.
Manawatu-Whanganui Civil Defence Controller Michael McCartney said the amount of water in the Whanganui River was close to being a 100 year flood event.
State Highway 3 has reopened but access is still restricted with police escorting small groups through.
Blocked roads are causing delays for workers trying to restore power to about 1000 homes in the Whanganui region.
A flooded substation and a large slip that brought down power lines had cut power to about 6000 properties last night.
Have you been affected by the flooding? Send your pictures or video to us by email iwitness@radionz.co.nz
Another night
The Wanganui District Council on Sunday said a total of 400 people had been evacuated and 244 of them had been through a welfare centre which opened on Saturday morning. They said most people went to stay with friends or whanau.
Many chose to leave their homes as the river spilled over its stopbanks early this morning after more than 24 hours of heavy rain.
Flooding at Onetere Drive, Whanganui. Left to right - Steph Locket, Maria Williams, Tracey Culver. Photo: Ian Williams
Dozens of homes on the eastern side of the river have been inundated by floodwaters with the Anzac Road and Putiki areas the worst affected.
Businesses along Taupo Quay in the central business district have also been flooded and the main bridge into the town is closed because it has been hit by logs.
Many properties affected by flooding and slips will need to be assessed by geotechnical engineers, then cleaned and limed due to sewage contamination.
The Wanganui District Council said these properties were not likely to be assessed until tomorrow at the earliest.
Evacuated areas in Taupo Quay, Anzac Parade and other flood and slip affected areas are cordoned off, and will be monitored by Police and Army personnel overnight.
If you have been evacuated, please do not return to your home under any circumstances.
An image of Whanganui taken by a resident. Photo: Diana Fowler
Rangitikei
Army unimogs evacuated six people from the township of Koitiata, in Rangitikei.
Koitiata resident Suzi Bryant said the army evacuated people who wanted to leave but most wanted to stay with their homes.
She said some of the town's 60 or so houses are badly flooded - and some owners will have lost everything.
Suzi Bryant said the roads in and out of the town were closed so the residents were isolated.
Waitotara
The entire village of about 60 homes and a pub full of people were evacuated late last night after a state of emergency was declared when heavy rain swelled the Waitotara River to dangerous levels.
An aerial photo of Waitotara. Photo: PowerCo
The river peaked at midnight with the high tide.
South Taranaki's Civil Defence controller David Lean said a helicopter was flying over the Waitotara Valley to check conditions in the more isolated areas.
While authorities said the threat of serious flooding in Waitotara had passed, they had major concerns about the stability of the bridge crossing into the town.
James Takarangi mops out his Waitotara home. Photo: RNZ / Robin Martin
South Taranaki Mayor Ross Dunlop said Waitotara remained a viable community despite suffering serious flooding for the second time in just over 10 years.
He said the people of Waitotara were a resilient bunch who have chosen to live there and the council would continue to support them to do that if that was what they want.
Mr Dunlop said it had however been devastating to see the amount of water and silt through the town today.
Authorities are still assessing whether residents can return permanently to the most affected homes.
Aaron Fitton and his cat Iggy. Aaron's Waitotara house is knee high deep in water. Photo: RNZ / Robin Martin
Roads
Some major highways in the lower North Island are being reopened after slips and flooding caused their closure.
State Highway 1 is now fully open after flooding closed it at the Waikawa River Bridge, between Levin and Otaki, but motorists are advised to take care.
Cars on State Highway 3 waiting to get into Whanganui. Photo: RNZ / Tom Furley
State Highway 3, between Whanganui and New Plymouth, has also reopened but authorities are advising against non-essential travel.
State Highway 3 between Bulls and Wanganui has also been reopened.
Work is also continuing on a number of small slips in the Manawatu Gorge, which is likely to remain closed for a few days.
The Pahiatua Track also remains closed but the Saddle Road is open, with efforts to restore access for heavy vehicles.
The Transport Agency said motorists needed to be aware of debris, slips, flooding, one lane restrictions and potholes which are widespread.