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The Whanganui River has burst its banks, flooding parts of the city and closing roads.
A Civil Defence state of emergency was declared yesterday after the region was lashed with rain.
Around 160 people have already been evacuated from their homes.
Radio New Zealand reported this morning the river had seeped through stopbanks overnight. The water level had dropped slightly since last night but a high tide is expected about 9am today.
Mayor Annette Main said most people had gone to stay with families and friends but there were emergency measures in place too.
"The river has been high for quite a long time, so there's concern about the integrity of those banks with such a long period of flooding.
Inside Wanganui River Stream building owner Peter Hardy says it's minimal damage pic.twitter.com/fR0Rk1K5Vx— Daniel Faitaua (@DanielFaitaua) October 15, 2013
Army personnel from Wanganui and Linton spent last night sandbagging the stopbanks of the Whanganui River.
Civil Defence Controller Kevin Ross said they assisted with road cordons.
The Red Cross emergency response team and the rural fire crews also provided support.
By 9pm yesterday 113 people had registered with the Civil Defence Welfare Centre and 18 people had been found temporary accommodation.
Wanganui residents were warned all flood waters should be considered contaminated after the sewerage system overflowed in some places.
Mr Ross said manhole covers lifted along Anzac Parade and the floodwater was contaminated with raw sewage.
Two state highways have been closed due to flooding.
State Highway 4 is closed between Raetihi and Whanganui, and police have said it was unlikely to open before 11am. Motorists should avoid the area.
State Highway 3 is also closed at the Whangaehu Bridge. Drivers travelling north must use State Highway 1.
Meanwhile, Ruapehu District Council chief executive and Civil Defence controller Peter Till said staff and contractors were busy clearing roads and assessing damage.
"Ruapehu residents are, however, being asked to continue to drive to the conditions and take extreme care on the district's roads which sustained quite a bit of damage in areas.
More than 25 incidents were affecting roads in the region, including flooding, drop-outs, downed trees and slips - some of which would take some time to clear.
About 200 homes in the central and lower North Island are still without power following Monday's stormy weather.
Lines company Powerco said at the height of the outages, more than 20,000 properties in Wairarapa, Manawatu, Whanganui, Coromandel and South Taranaki were without electricity.
The majority of homes were back online, however about 200 properties still had no power.
Powerco network operations manager Phil Marsh said trees had caused the majority of the power cuts.
"Many of the power cuts could have been avoided if people had contacted suitably qualified tree trimmers to have their trees cut or trimmed before they caused a problem."
"Residents should contact their retailers and let them know if they are still waiting for the electricity to come back on. While crews are working to get everyone's supply back on it may be helpful to be pointed to individual properties."