The 55-year-old man, understood to be the victim of a home invasion, was admitted to Dunedin Hospital.
A police cordon was in place at the Church St property last night.
Two Allied Security staff manned the cordon from about 5.30pm yesterday.
Detectives left the scene about 6pm and were expected to return this morning.
The injured man was the sole tenant and had been renting it for "a number of years'', owner Michael Philpott said.
Mr Philpott visited the property following the incident but police did not provide him with details of what took place, he said.
The address looked to be unoccupied when the Otago Daily Times visited last night.
Senior Sergeant James Ure, of Dunedin, directed all questions to the police media centre in Wellington.
Police were called to the scene at 3.05pm, a police spokeswoman said.
She did not believe an arrest had been made and could not confirm the incident was a home invasion.
It was also unclear how many people were being sought by police in relation to the incident.
"Police are investigating the incident and no further information is available at this time,'' she said.
The injured man was taken to hospital by St John ambulance about 3.15pm in a serious condition, St John communications adviser Ian Henderson said.
Neighbours spoken to by the ODT yesterday afternoon said they did not see or hear anything out of the ordinary.
