"There was a front moving across and there was a large storm at the time," said Phillips.
Fire crews from Mangakino, Benneydale, Tokoroa and Otorohanga were battling the blaze in the single-storey building.
Meanwhile, at Manukau Heads, three neighbouring houses had been struck by a bolt. Four fire crews were headed to the remote west coast properties.
The Fire Service said they were called to three properties on Kohekohe-Karioitahi Rd, Waiuku, about 5.30am.
The roof of one house was badly damaged.
"One property, as a result of being struck by lightning, had damage to the roof - which resulted in a water leak, so the brigade assisted there," a spokesman said. "The second property had smoke showing from power sockets and lighting fixtures and the third property had minor flooding."
Water was now leaking through the roof of one of the hit homes.
The settlement of Mangakino has also been lashed by stormy weather. Flooding and a lightning strike have hit the main telephone network before dawn.
Phillips said fire crews encountered flooding leaving to fight the Pureora blaze.
A strike had triggered the fire alarm at the Mangakino Telephone Exchange and the town was now without landlines, he said.
Mangakino Century 21 real estate agent Christine Stevens said they experienced some heavy downpours overnight. There was a bit of water around but as it had stopped raining by about 7am she expected it to dissipate pretty quickly.
A pair spending the night in their vehicle at the Ruakuri Reserve awoke to find water coursing through their parked vehicle.
A police spokesman said firefighters walked the pair to safety through the fast-rising floodwaters that had swamped the scenic reserve's car park.
Te Kuiti fire chief Phil New said the two men, aged in their 20s, from were California and as it was still dark and they were unsure what to do, they called emergency services for help.
He said firefighters waded through water more than a metre deep to rescue the pair - who were now speaking with local police - from their rented Toyota stationwagon.
New said the rain had been heavy all night and hadn't shown any sign of abating.
MetService forecaster Tom Adams said there had been 30 lightning strikes on land.
The storms would give way to showery weather and fresh thunderstorms would hit later in the day, he said.
