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He was Bruce James Cochran (53), of Albert Town.
Police were yesterday reluctant to confirm Mr Cochran's identity, saying dental records would be required to positively identify him.
Residents in the house in front of the flat yesterday said they were ''as sure as they can be'' of his identity.
Police today said a scene examination was progressing well, and a post mortem examination would be conducted in Dunedin this afternoon.
Detective Senior Sergeant Colin Blackie yesterday said there was ''nothing at this stage indicating foul play, but you can't cross that out''.
Experts from ESR in Christchurch and fire investigators from Dunedin were at the scene yesterday and it was expected gas and electrical experts would also examine the flat.
At the scene, Fire Service East Otago commander Laurence Voight said Wanaka firefighters found the body at 4.30am.
The fire was well involved ''and after searching for a couple of minutes they located a person inside, in the rear bedroom''.
Mr Voight said attempts were being made to contact North Island relatives of the victim.
A nearby resident, Kylie Arnesen, said she was alerted to the fire by her 6-year-old dog Zoe, who had been sleeping outside.
Ms Arnesen said the fire was ''well ablaze'' by the time she saw it and rang emergency services.