A severe heavy rain and gale weather warning is in place for much of the country as widespread flooding affects farmers, drowning lambs, dousing paddocks, and making driving difficult.

Heavy rain is forecast today for Fiordland and the Southern Alps and the central and lower North Island, with already swollen rivers and streams threatening to burst their banks.

The flooding has already led to road closures in some areas and Manawatu and Horowhenua farmers awoke this morning to widespread flood that turned paddocks into mini lakes.

In the northern Wairarapa, the main road between Eketahuna and Pahiatua was closed by extensive flooding. There were no alternative routes available as local roads were also flooded.

Bronwyn McIntyre, who farms at Shannon in the Manawatu, said she had about 20 lambs die in the flooding.

"We tried to move them as fast as we could but the water came up too fast and the lambs drowned," she told the Manawatu Standard.

There had been flooding north of Shannon and some paddocks near Otaki, 70km south of Palmerston North, had flooded on to the highway, Levin Sergeant Esmae Laird said.

"Drivers should absolutely drive to the conditions and remember that even if rain has subsided, there might still be flooding for some time," Ms Laird said.

The Mangahao River in the Manawatu was at its flood levels and other rivers in the area were rising, Ms Laird said.

Civil Defence has activated its emergency plan for the Hutt River north of Wellington after exceptionally heavy rainfall overnight.

Police said there was concern that the Hutt River may overflow and Block Road at Melling, near the Lower Hutt city centre, had been closed with the possibility that other roads may also be affected.

State Highway 94 between Te Anau and Milford Sound was closed by flooding and rain has caused slips and surface flooding to State Highway 57 between Levin and Palmerston North.

High winds in exposed parts of Wellington and the Wairarapa were expected to ease today after they caused havoc on the roads yesterday and today.

An ambulance was blown over while attending a crash in which a van was blown over in severe winds in the Wairarapa yesterday.

The driver of the van and two paramedics suffered minor injuries and were taken to hospital.

A bus was also a victim of the high winds when it was blown off the road near Dannevirke this morning.

The driver was the only person aboard and was not injured.

The winds have also brought trees down on a few small roads around Dunedin.