Detective Sergeant Mark McCloy said there were still other residents unaccounted for and enquiries were ongoing to try and find them.
Crews responded to the fire at a single-storey house in View St, Manapouri about 3.30am.
Southland Area Commander Inspector Mike Bowman said earlier it was unknown how many people were at the address when the fire started.
Stuff is reporting a woman, child and a man live at the property.
Police and Fire and Emergency New Zealand (Fenz) personnel are on site with a fire investigator.
Neighbour Allan Biggs said he did not know the residents but was woken up by sirens.
"With the siren going off, eventually curiosity got the better of me and I got up and just surprised to see the house well alight across the road," Biggs said.
A few neighbours had gathered on the street and he could hear the fire crackling, he said.
"We do get the odd callout of a fire engine in the middle of the night, but it's usually a traffic accident or something like that, nothing like this before."
A Fenz spokeswoman earlier said crews from Te Anau and Manapouri responded and found the house "well-involved" when they arrived.
Det Sgt McCloy said police would work alongside Fenz to conduct a scene examination and enquiries over the next days.
"The cause of the blaze continues to be unexplained.
"Further details will be provided when they become available," he said.
- ODT Online/RNZ
