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One Taupo house, it was reported, had to be evacuated after a "creek became a river" around 8pm.
A thunderstorm and high winds hit the tourist town overnight on Thursday with reports of flash flooding and a tree being hit by lightning on a rural property.
There have been unconfirmed reports of buildings having roofs blown off and a 60m tornado striking the suburb of Paetiki.
The MetService couldn't confirm the tornado reports but forecaster Geoff Sanders said it could possibly happen.
A heavy downpour hit Rotorua between 4.30am and 5am yesterday but there have been no reports of damage or flash flooding.
A severe thunderstorm watch was issued by the MetService for the Bay of Plenty yesterday.
Thunder hit Rotorua about 2pm and 5pm for short periods.
Phil Parker, Taupo District Council emergency response manager and principal rural fire officer, said a tree at the top of a hill on a Tukairangi Rd farm was hit by lightning just before 9pm on Thursday, killing sheep taking shelter.
Rugged terrain made if difficult for rural fire fighters to get to the site.
Between 8pm and 9pm on Thursday night 24mm of rainfall was recorded.
The fire crew were at the property for more than two hours tackling the small fire caused by the lightning strike, Mr Parker said.
"It was difficult to get to," he said.
"We had some pretty heavy rain and a bit of flash flooding in some remote rural places."
He didn't know anything about a tornado but said council had an emergency plan in place in case the predicted thunderstorm hit the tourist town during the Chiefs versus Hurricanes game at Owen Delany Park last night.
Staff were on standby and emergency lighting had been set up in case of any power cuts, Mr Parker said.
"We've been told to expect a lot more rain and high winds with another serious thunderstorm on its way," he said.
"Some of the places being hit are quite isolated."
Mr Sanders from MetService said while another thunderstorm was due to hit both Taupo and Rotorua yesterday, most of the weekend would be mainly fine with some heavy rain expected this afternoon.
"There will be some heavy localised heavy downpours Friday with morning cloud and long fine periods on Saturday for Taupo," he said.
"It will much the same in Rotorua with some isolated afternoon and evening showers for Rotorua on Saturday.
There could be some quite heavy downpours."
Meanwhile, 33mm of rainfall was recorded in Rotorua overnight on Thursday but the CastleCorp were not called to any incidents of flooding.
Springfield weatherman Brian Holden said despite the dry start to the month, 56mm of the 100mm of normal rainfall for the month had already been recorded for February.
More was on the horizon, he said.
The sky above Rotorua was rather bleak as he looked across Lake Rotorua yesterday morning.
"There are signs of instability. You can see it in the clouds forming," he said.
"It might not amount to much but this is what we can expect with thunderstorms. It definitely looks unsettled."
Last night's thunderstorms were tracked mostly around northern parts of Auckland and central eastern parts of the North Island, WeatherWatch head weather analyst Philip Duncan said.
At the peak of the storms a few thousand lightning strikes were detected in an hour.
Downpours led to the Fire Service being called to more than 40 incidents, mostly flooded homes, between 6.30 and 7.30 last night in Glen Eden and Titirangi.
Fire Service spokesman Paul Radden said extra appliances were sent to the suburbs, including those equipped with machinery to pump floodwaters.
One elderly man was taken to Waitakere Hospital with chest pains after his apartment was one of three flooded on Captain Scott Rd.
Ashok Sudhakaran photographed his neighbours' cars swamped by floodwater at Atkinson Rd in Titirangi after a "huge amount" of water cascaded down a nearby hillside.
He said he was inside his house nearby when the area was hit for about half an hour by the heaviest rain he had seen in Auckland.
Additional reporting NZ Herald