WeatherWatch said more than 1160 lightning strikes were recorded from 1am to 2am, mostly between Whangarei and Auckland.
Fire Service northern communications shift manager Scott Osmond said there had been between 15 and 20 weather-related calls in Auckland since midnight and there was minor flooding in the Auckland Isthmus area.
In Tauranga, gusty winds lifted roof tiles from a few homes, Mr Osmond said.
The bad weather also forced a rescue helicopter to abandon an operation to winch a badly injured man to safety in Northland yesterday.
MetService said Auckland received 52mm of rain overnight.
MetService duty forecaster Rochelle Fleming said the weather would be unsettled for large parts of the country for the rest of today and tomorrow with showers in many areas.
"There is the risk of isolated thunderstorms for Taranaki, Nelson [and] Marlborough Sounds this evening.
"Otherwise, showers [are forecast] for a lot of the western areas of the North Island. There's a heavier band going through Rotorua just at the moment."
Tomorrow would be "reasonably showery" in the Taranaki region down through to Kapiti, Ms Fleming said.
However, more fine spells were forecast for Auckland and areas further north.
"Heading into Tuesday we've got a deep low that comes down from the north, we're expecting it to lie near to Cape Reinga midnight Tuesday and with that there'll be strengthening easterlies over most of the North Island, gales for a lot of places and possibly severe gales especially through the western areas."
The low was also expected to bring heavy rain, however temperatures would remain reasonably warm, Ms Fleming said.
WeatherWatch spokesman Philip Duncan said heavy showers were coming back to hit the centre of New Zealand.
"Coming in towards Taranaki and Cook Strait at the moment there are some more thunderstorms and some heavy showers also around Rotorua and the northern Southern Alps."
The system would take through to tomorrow to die out, Mr Duncan said.
"There'll be sort of showers around much of the country tomorrow and other areas will be improving.
"That's all ahead of a storm that's coming out of the tropics for Tuesday."
Meanwhile, 150 rural Canterbury customers with lines company Orion are still without electricity, 12 days on from one of the most destructive storms to hit the region in 40 years.
The storm originally took out power to 28,000 Orion customers.
Orion chief executive Rob Jamieson said all the company's crews and many others from outside the region were doing all they could to get power back on.
"It is slow progress as the repairs we are onto now are taking many hours to complete yet they only bring back power to a few customers. For those still without power it is a very frustrating time and I thank these customers for their ongoing patience and tolerance," he said.
