Evacuations are still likely to take place, but later in the day, says the Whanganui District Council.
An intense band of rain has now passed further to the north of Whanganui than expected.
A Civil Defence Emergency team remains on standby.
Further updates are expected after 8am when the Civil Defence Emergency Management team will attend a conference call with the Regional Controller.
By 10am council expects to have the latest Metservice dataset and hydrology analysis on the weather.
People to choose to evacuate themselves from their homes are being advised to check in with a Civil Defence Centre. either in person, or by calling Whanganui District Council on 06 349 0001.
Two Civil Defence Centres are open:
St Paul's Church in Guyton Street
Whanganui Girls College in Jones Street, Whanganui East
Council urges people to stay off the roads.
"If you do not need to evacuate, we recommend you stay home and avoid travel. Weather conditions are still cause for concern."
All Whanganui schools are closed today, Wednesday 5 April 2017.
There may be a number of other roads closed throughout our district due to surface flooding and slips.
Horizons Regional Council activated the Moutoa floodgates at 2.15am this morning, and have deployed flood defences barriers at Whanganui Yacht Club, Kowhai Park and Balgownie due to high water levels in the Whanganui and Manawatu Rivers. Whangaehu and Turakina also remain on high alert.
Horizons controller Craig Grant says the weather patterns continue to change. Less rain that expected has fallen over the past few hours, resulting in reduced and delayed river levels compared to last night's 10.30pm update.
"While this still remains a significant event, it is now predicted to be on a smaller scale than that of the 2015 flood event," Mr Grant said.
"We now expect Whanganui River to peak at Pipiriki at 13.8m around 11pm this evening. This will result in an 8.5m peak at Town Bridge at 6.45am Thursday morning.
"Whanganui District Council declared a state of emergency yesterday and has been contacting people who live nearest the river via door knocking and phone trees. They were planning to evacuate people at 6am, however further assessment of expected weather and river level modelling may delay this urgency."
The two Civil Defence Welfare Centres at Whanganui Girls' College and St Paul's Church will be open from 6am, and schools in the district are closed today.
Rangitikei District Council has also declared a state of emergency and advised residents of evacuations in the Marton area overnight. Their Whangaehu and Turakina community response plans have been activated.
"Whangaehu and Turakina property owners were contacted about the flooding of farmland, originally expected to occur this afternoon. This timeframe has now been changed to later this evening with Whangaehu expected to peak at 10m at 7.30am tomorrow morning," says Mr Grant.
"Our Emergency Coordination Centre staff will continue to monitor as SH3 may potentially close tomorrow at approximately 10am.
"Farmers who use the Moutoa spillway were contacted prior to the floodgates opening this morning.
"The Makino is expected to peak 1.9m at 12noon today, and again 2.4m at 12.30am Thursday. Farmers who use the Makino spillway will be updated as gate operations are likely.
"We continue to be in constant contact with Whanganui and Rangitikei District Councils, as well as well as agencies including NZTA, NZ Police, NZ Defence Force and the Fire Service."
Horizons said it would issue another update after 10am.