Police had surrounded a rural property where a man being sought over alleged firearms offending was holed up.
In a statement shortly before 2pm, Inspector Marty Gray said officers entered the house about 10:15am and found the man dead inside.
He said police, including specialist squads supporting local staff, had been working to resolve the matter safely.
"While this is not the outcome police would have hoped for, I want to thank the frontline staff and specialist teams for their hard work in responding diligently to this very lengthy incident.
"The man’s family are being supported at this very difficult time."
He said the death would be referred to the Coroner.
The police presence on Hunt Rd, where officers have been stopping traffic, was earlier winding down, and the tactical units have withdrawn.
After a manhunt involving multiple officers, police last night said they had found the person they were seeking in connection with alleged firearms offending in the Clutha area.
"Police have engaged in dialogue with the person, who is believed to be alone, at a rural Clutha property.
"The situation is contained and there is currently no risk to the public."
Yesterday, police descended on Hunt Rd, about 5km north of the rural settlement of Owaka, establishing cordons in their search for a "person of interest".
About 15 armed police were at the scene, along with two ambulances, several dog teams and what was believed to be a negotiation team.
