The 50 people in the Tararua town of Pahiatua who were evacuated from their properties because of the threat of flooding from the Mangatainoka River have returned home.
The river peaked on Monday evening without flooding, but several rivers and streams, including the Manawatu, are still to peak.
State Highway 2 between Eketahuna and Pahiatua, as well as the Pahiatua Track, are closed and slips, and floods are blocking State Highway 3 in the Manawatu Gorge.
State Highway 56 is also closed at Opiki.
Manawatu Whanganui Regional council's emergency manager, Allan Cook, says it will take some time for the water to drain to the sea.
He says it will open the Moutoa floodgates on Monday night to relieve flood flows on the lower Manawatu River. Several days of heavy rain in the Tararua and Ruahine ranges have necessitated the measure, which will divert water over flood plains north of the town of Shannon.
He says the flood plains are used for grazing and farmers are being told to move their stock.
Mr Cook says floodgates built after the 2004 floods in Feilding will be opened for the first time.
He says another floodway system may have to be opened north of Palmerston North, potentially blocking the highway out of the city.
Mr Cook says the Manawatu River flooded State Highway 56 near Opiki on Monday evening.
Horowhenua District Council says flooding has forced the closure of the Levin water treatment plant. Residents in Levin, Shannon, Mangaore and Tokomaru must boil any water before drinking.
The Ruamahanga River in south Wairarapa is at flood level and is expected to spill over into its floodway later on Monday.