More than half of government departments were unable to provide "credible and quality information" in their financial reports, Business Day reported on Tuesday.
This threatened the government's ability to carry out its obligations.
Only 43% of national departments achieved clean audits, and only 18% of municipalities, the AG told a public sector forum, convened by the Institute of Internal Auditors, on Monday.
Supply chain management regulations were adhered to by only 43% of national departments and 22% of municipalities.
Accountant General Freeman Nomvalo said for the last three years government departments had doubled their irregular expenditure annually, which created opportunities for public officials to loot funds.
"It opens the way for tender-rigging to become the order of the day."