MetService is warning that more heavy rain is on the way for eastern parts of the country until the weekend.
A rainfall warning is in place for the hills and ranges between the Napier-Taupo Road and and Manawatu Gorge, eastern Marlborough and Canterbury north of Cheviot.
In Marlborough and North Canterbury, where the land is already saturated after heavy rain in the last two days, more rain is expected throughout Thursday and Friday and may become heavy again from Thursday night.
Forecasters warn this may lead to rising streams and rivers and possible surface flooding and slips.
Roads still closed in Marlborough
About a dozen roads in Marlborough are still closed Wednesday evening due to flooding, but the rain has eased.
The Marlborough District Council's assets and services manager, Mark Wheeler, says some areas have received up to 130 mm of rain over 24 hours.
There is some damage to farmland and vineyards, but no reports of houses being flooded.
Mr Wheeler says 12 roads are still closed in the south and south-eastern part of the district, but in most cases alternative routes are available.
It is expected most roads will re-open on Thursday morning.
Meanwhile, flood controllers have been stood down in Canterbury on Wednesday evening after river levels dropped.
High winds are now causing problems on the West Coast with the Transport Agency warning drivers on State Highway 6 between Harihari and Haast to be careful.