SA Health said the overseas-trained doctor worked at the Port Augusta Hospital, in the state's mid-north, between April 24 and May 2 before being removed from the premises.
The Australian Health Practitioner Regulation Authority and Australian Medical Board have since offered the doctor provisional registration with conditions.
But the bungle has been referred to SA Police, the Australian Health Practitioner Regulation Authority and other investigative bodies for further action.
A locum doctor supervising at the emergency department has also been stood down over the incident.
SA Health chief executive Robyn Lawrence said she had commissioned an independent inquiry, promising to make any findings public.
"It is completely unacceptable that an unregistered doctor could be in an environment where they have access to patients, without providing their credentials or registration," Dr Lawrence said.
"That is why I have commissioned a full independent investigation into how and why this occurred to make sure it never happens again."
It is understood the doctor treated at least 15 patients, with authorities now contacting each of them to discuss their care needs and to determine if a follow-up appointment is required.
SA Health said it was not aware of any adverse clinical outcomes.
