MetService is advising this may cause streams and rivers to rise rapidly. Surface flooding and slips are also possible and driving conditions may be hazardous.
As the low continues to track southward on Friday, the wet weather will begin to disappear along with it.
This is not before the rain spreads to Marlborough and Canterbury, while conditions start to improve over northern areas of the North Island.
By Saturday, the low will be moving away to the east, giving way to a relatively pleasant long weekend for much of the country but showers will linger.
"New Zealand will be on the edge of a high-pressure system this weekend, keeping us mostly settled but this isn't quite enough to keep the rain entirely away as we still expect bouts of showery weather for most areas, especially for the north and east," Fernandes said.
Temperatures will remain near average for this time of the year and even tend slightly above normal for many areas.
Most notable will be Central Otago's maximum temperatures, which are forecast to peak close to 20C this weekend. This is about 5C above their normal for late September.