Manawatu-Wanganui Regional Council says it has successfully lowered water levels using a floodgate built to avoid a repeat of devastating floods in 2004.
The Makino gate was completed in March last year on the Makino Stream in Feilding, an area badly affected by the earlier floods.
It was closed for the first time on Monday, to divert rising waters into the Reid Line spillway.
The Moutoa floodgate was also used, to lower levels in the Manawatu River overnight.
The council says some farmers are concerned about water pooling on nearby properties, but that is expected to clear over time.
Farmer Keith Riley says the damage is not as great as that in 2004.
Mr Riley's farm became famous in 2004, when cow # 569 saved his wife, who had been swept away by floodwaters.
As a result of heavy rain in the Ruahine and Tararua ranges on Monday, the Mangatainoka River, which skirts the town of Pahiatua, threatened to burst its banks, before peaking at 5pm.
Up to seven houses were flooded. Fifty residents were evacuated from their homes for several hours.
Tararua District Council says an assessment will be made of the damage to roads and infrastructure, and the flooded houses.
Civil Defence controller Peter Whimsett says the pumping station at the Fonterra dairy factory was taken out by the river's rising levels.
He says the factory is relying on its water reserves and tankers being brought in.
State Highway Three through the Manawatu Gorge was reopened late on Tuesday afternoon after being closed by slips and flooding.
Earlier, State Highway Two from Eketahuna - Pahiatua, State Highway 56 at Opiki and State Highway One at Marton, were also closed.
Care is required on State Highway 57 from Levin to Linton and State Highway Three at Ratana.