"This amount of rain may cause rivers and streams to rise rapidly, slips and surface flooding," MetService said.
Further rain was expected today in Marlborough and the Wairarapa but those downpours would not be prolonged or heavy, MetService said.
The rain was expected to ease tonight.
Flooding closed two state highways in the North Island this morning.
The New Zealand Transport Agency said State Highway 56 from Opiki to Palmerston North was closed and motorists should use SH57 as an alternative route.
Further north, the Napier-Taupo Rd (SH5) was closed because of flooding and slips, and there were was no recommended detour route.
Flooding earlier this week inundated at least 50 properties in the Gisborne area.
Heavy rain causes major slip in Bay of Plenty
Heavy rain has caused a major slip which has closed a rural road north of Lake Rotoiti in the Bay of Plenty.
Maniatutu Rd, between Otaramarae and Pongakawa, was closed to traffic on Wednesday afternoon.
The slip is about 9km north of the Rotoiti end of Maniatutu Rd, near the Rotorua Lakes Council and Western Bay of Plenty District Council boundaries.
Rotorua Lakes Council roading contractors are currently working to clear the slip but it could be several days before the road is safe to re-open.
The council is advising those with medical conditions to make precautionary arrangements in case of a medical emergency.
Emergency services and the New Zealand Transport Agency have been informed of the road's closure.