The weather system that brought flooding to the East Coast now is tracking across the lower North Island, causing rising river levels and closing roads.
The Manawatū River rose sharply after overnight rain and the Moutoa floodgates have been opened.
Horizons Regional Council river manager Raymond Strong said the river had peaked at about 5m.
"We've been monitoring river flows during the night, holding off opening the gates as long as we could," Mr Strong said.
"We made the decision this morning to open those gates and just relieve pressure on that lower Manawatū River system."
River flows were expected to peak in Palmerston North this morning and the river level would start to reduce during the day.
Rising river levels have closed the Waihenga Bridge on State Highway 53 - the main road out of Martinborough.
The town was not cut off as there were three other exit routes motorists could take, a South Wairarapa District Council spokesperson said.
The low tracks southeast across the lower North Island today and moves out to the east by Thursday, further heavy rain is expected. The heaviest falls are now expected over the central plateau, the Kaikoura Ranges and the north Canterbury Hills. https://t.co/qHyE5zhh6X ^MBTA pic.twitter.com/zBa5BCPdMd— MetService (@MetService) June 12, 2018
The Whakapapa ski field is closed after heavy rain and high winds caused snow levels to fall.
SH3 Ashhurst to Woodville (Manawatū Gorge) and SH5 Taupō to Napier are closed due to slips.
Road damage between Te Araroa to Tolaga Bay is causing delays.
In the South Island, State Highway 1 through Kaikōura is closed because of debris brought down on the road in heavy rain.
The Transport Agency hopes to have access via Waiau restored by early afternoon.
Flooding in Christchurch has closed part of Clarendon Terrace and Maces Road and a slip has closed Goughs Bay Road.