The man appeared in the Dunedin District Court yesterday afternoon and was remanded in custody, without plea, until November 23.
Judge Jim Large also gave the man interim name suppression.
On the day of the fire, neighbours said two or three homeless people slept in the derelict house periodically, and it was initially feared someone may have been trapped in the fire.
However, police later confirmed there were no people in the building at the time of the fire.
The Kensington property was being demolished after Christopher Paul Bonisch (51) was killed in a fire there last year.
Last month, WorkSafe placed a prohibition notice on the property, halting demolition over concerns about unsafe work at height and the possible presence of asbestos.
Following the arrest of the 57-year-old, Detective Senior Sergeant Rob Hanna, of Dunedin, said he was "thankful" no-one was injured in the fire.
"However, several adjacent properties were damaged."
Despite the arrest, Fire and Emergency New Zealand Otago district assistant commander Craig Geddes said the investigation into the cause of the blaze was ongoing because of the extent of the damage.
"There are a number of complexities involved in that fire — the period of burning and so forth.
"We’re working with police and ESR [Institute of Environmental Science and Research] on it.
"It’s quite a big operation so I would suggest it’s going to be a bit of a time delay before we can get answers about that one — at least another week or so."
The Rent Shop owner Denise Robinson said one of her flats next to the boarding house, was badly damaged by the blaze and the occupants had to be removed and placed in alternative accommodation.
She said it was not known when, or if, the tenants could return to the building.
The building remains boarded up at this stage, she said.
