The 66-year-old was discovered about 4.40pm after police were called to the property at Port Neill to check on his welfare.
Detective Inspector Brett Featherby said the investigation was “in its infancy”.
“The investigation is in it’s very very early stages, we had members arrive there this morning, we are trying to determine the relationships between the persons,” he said.
Featherby said the exact relationship between the two men was still being determined but said it was not a random incident.
The 28-year-old man was refused bail and will appear in the Port Lincoln Magistrates Court tomorrow.
