Flooding has closed roads around Manawatu, including State Highway 3 through the Manawatu Gorge and part of SH56.

The Manawatu Gorge would be closed for several weeks after rising river waters undermined a temporary road.

The road is closed in both directions, with an alert issued at 5am by the New Zealand Transport Agency.

"The gorge road has been closed because the heavy rain has caused the river levels to rise, which has washed away some of the old slip material under the temporary road, and we've had to close it for safety reasons. It looks like there is a lot of work to do and the road is likely to be closed for several weeks," a spokesman said.

Motorists are being urged to detour along Saddle Rd or the Pahiatua Track.

A temporary road was opened in the gorge on May 31, for the first time since August 2011 when a series of landslides closed it.

NZTA Palmerston North state highways manager David McGonigal said it was important to note the closure was not because of another slip.

"We always knew that if the river flooded there was potential (the road) would wash away. We are disappointed but we always knew it could happen.

"We can only deal with what the weather gives us.

Flooding has also closed State Highway 56, where it crosses the Manawatu River, this morning.

NZTA website reported the road was closed about 8.30am due to flooding across the road.

A detour is in place for motorists travelling through the area, but there is no indication when the road is likely to reopen.

Meanwhile Horizons Regional Council has issued a warning for farmers in the Moutoa floodway to move stock and drop fences in preparation for a possible gate opening today.

Horizons emergency manager Shane Bayley said the council's Emergency Operations Centre had been activated and staff would monitor the situation throughout the day.

"We've been keeping a close eye on the Region's river levels, the rain is easing off but we do have a crew on standby to operate the Moutoa floodgates if required," he said.

"Farmers have been asked to remove any stock from the floodway by 1pm today so we can open the gates to remove pressure on the Manawatu River if needed. This is a precautionary measure."

The river is expected to peak at 5.2m at Horizons' teachers' college monitoring site at around 1pm and Horizons had no concerns about river levels in the rest of the region.

The Opiki floodway is currently underwater. Members of the public are being advised to exercise caution when driving and check maps.aa.co.nz/traffic/roadwatch for information on road closures.

- © Fairfax NZ News