South Australia's corruption watchdog is “very confident” there is corruption in the state's health department, but it needs more resources for a thorough investigation.

Independent Commissioner Against Corruption Bruce Lander says it has been almost impossible to determine the true extent of the issues at the troubled department, because record-keeping is so poor.

He says there are inappropriate arrangements between the department and clinicians and between the department and other suppliers and contractors.

“We know what the problems are, we just find it frustrating that in the course of our investigations to find that we cannot identify, with the necessary precision, the arrangements that were entered into between health and its employees,” Mr Lander says.

“Record-keeping within health is so bad and the arrangements are so vague that you can't precisely say what the arrangements were or should have been and it's very difficult to identify corruption.

“Better record-keeping, in my opinion, would identify more corruption.”

The commissioner said he wants to probe the practices, policies and procedures across the health bureaucracy, but the agency is enormous.

“I just don't have sufficient resources to do the whole of health at the moment,” he said.

Health Minister Stephen Wade welcomed a broader inquiry into the department, but said the commissioner must do what he can with his resources.

The approval of the attorney-general and the treasurer would be required to seek any extra funding.

SA Health has been slammed over operational concerns, and issues relating to overcrowding at hospital emergency departments and continual budget blowouts.

While he acknowledged some concerns with SA Health, Mr Lander said he did not believe corruption was systemic across the SA public sector.

However, he said the sector is “plagued” by maladministration and poor conduct.

“Both of which foster environments that make individual corruption possible and, in some instances, make it extremely difficult to detect,” he said.