"Those [under the high risk] are the places that we are most likely to see some strikes or at least hear some thunder," Clark said.
The thunderstorms might produce localised downpours of 10 to 25mm/hr - "so that's an instantaneous rain rate, that can cause surface flooding".
There is a heavy rain watch in place for Waitomo, Taumarunui and the headwaters of the Whanganui river this evening - where there is more likely to be "prolonged rain".
That could cause rivers to rise rapidly and remain that way, she said.
Auckland could expect a few showers, but rain for a time this afternoon, she said.
"The trend is that it will be getting worse as we head into the later part of the day.
"Tomorrow is going to be the wetter day for Auckland."
And while that rain is expected to ease later in the weekend, turning to cloud and scattered showers on Sunday, rain will return on Monday.
Main centre forecasts today
Whangārei
Mostly cloudy. Showers clearing evening. Northwesterlies. High 23C, low 17C
Auckland
Mostly cloudy. Occasional showers, but rain for a time this afternoon. Northwesterlies. High 23C, 17C
Hamilton
Periods of rain, some heavy tonight. Northwesterlies. High 21, 16C
Tauranga
Mostly cloudy with occasional rain. Westerlies. High 22C, 17C
Wellington
Mostly cloudy. A few showers, mainly north of the city, turning to rain this evening. Northerlies. High 18C, 13C
Christchurch
Fine spells increasing. Northeasterlies developing this afternoon. High 15C, 10C
Dunedin
Mostly cloudy, rain at times. Northeasterlies. High 12C, 10C
Source: MetService