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Fire investigator Mark Bredenbeck said the house in White Sow Valley Rd, about 15km east of Ranfurly, was not connected to electricity and had been unoccupied for some years.
Lightning could not be discounted as the cause, he said.
A MetService spokesman said while there had been no lightning strikes in the area at the time the blaze, there had been a large number around midnight.
A Fire and Emergency New Zealand spokesman said a call was received at 4.20am from a person who could see fire on the hill from a distance.
Fire crews from the Naseby and Ranfurly volunteer fire brigades attended.
When crews got to the scene, they found a house fully ablaze, he said.
Crews worked for more than three hours to protect neighbouring structures and prevent the fire from spreading, he said.
Its owners live in the North Island.