Pretoria - Auditor general Terence Nombembe has concerns about President Jacob Zuma's office complying with laws and regulations.
According to the 2010/11 General Report on National Audit Outcomes released in Pretoria on Monday, he had the same concerns about all but three of the 39 national government departments.
The other three departments were those of environmental affairs, public enterprises and science.
Nombembe, who released the report at a National Press Club briefing, would not be drawn on his specific concerns about the presidency - which received a financially unqualified audit report, but with findings.
Most other government departments received similar reports. Nine departments received qualified audit reports. Only the department of public works received a disclaimer.
According to the report, a disclaimer is issued when the auditor cannot form an opinion on the financial statements.
This can happen where the entity being audited conceals or fails to provide relevant information, is involved in litigation, or if its status as a going concern is threatened.
A financially unqualified audit with findings was issued when entities had not "fully addressed deficiencies in their reporting on predetermined objectives and/or compliance with laws and regulations".
Nombembe said he was happy with the overall improvement in the performance of government departments and the "commitment" of their leadership to getting clean audit reports.
"Leadership has risen to the commitment (of obtaining clean audits). The biggest area of concern is when it comes to supply chain and procurement. The rules are known and the expectations are known."
One of the "biggest weaknesses" that government departments had was in their information technology systems.
Nombembe said the findings where there were concerns did not necessarily relate to a loss of money.
Government departments were willing to implement recommendations.
"This was one year where there was no debate," he said.
The report indicated that the Road Traffic Management Corporation, the National Arts Council of SA and the Technology Innovation Agency had received adverse audit reports.