This emerged when Auditor General Terence Nombembe tabled the outcomes of his audit of the department for the 2012/2013 financial year, according to the report.
The findings were presented to the provincial standing committee on public accounts last week.
Nombembe found the then department accounting officer Ndoda Biyela failed to effectively prevent irregular spending of more than R5.7bn and wasteful spending of more than R408 million.
The department overspent more than R324m to acquire goods and services.
Other irregular spending included R270m on security contracts which contravened supply-chain protocol, R825m on unsolicited tender bids, and R120m on infrastructure irregularities.
The auditor general said the department was unable to meet its contractual obligations and pay service providers within 30 days as required by law, the newspaper reported.
He also found the department appointed employees without following proper process and could not confirm the department had received over R2bn in revenue from patient payments and neighbouring provinces, The Star newspaper reported.