"Around the Auckland area has just been a line of showers, there hasn't been any lightning yet," Coutts said.
"The rest of the North Island is pretty well fine, and in the South Island we have a cold front making its way northwards with rain going through north Otago at the moment."
Showers were also taking hold in Southland and up the West Coast, while Canterbury, Nelson and Marlborough remain fine.
Coutts said the thunderstorms were expected to fizzle out by this evening, but showers in the South Island would continue overnight.
A snowfall warning has also been issued for the Crown Range Rd, between Queenstown and Wanaka overnight.
Rotorua Lakes Council is warning residents to check their spouting and drains.
"Rainfall may reach up to 40mm per hour which is predicted to ease gradually by tonight," it posted on Facebook.
"It may pay to check your spouting and drains around your home are clear as expected rainfall can cause flash flooding especially in low-lying areas like streams, rivers and narrow valleys, and may also lead to slips."