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"The amount consists of unauthorised expenditure, irregular expenditure as well as fruitless and wasteful expenditure accumulated over a period of seven years," department spokesperson Simon Zwane said in a statement.
Earlier, The Star newspaper reported that the department could not account for more than R12bn, nearly half its budget.
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 R408m.
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.
Zwane said the amount of just over of R6bn for unauthorised expenditure was an accumulation of balances from previous years.
"The unauthorised expenditure incurred during the 2012/2013 financial year is R324 474 000," Zwane said.
The overspending was linked to emergency medical services, provincial hospital services and central hospital services programmes, he said.
Zwane said the amount had significantly reduced from previous years which was good for the department's turnaround strategy.
He said that the R408m spent on fruitless and wasteful expenditure was also a combinantion of balances from previous years.
"The fruitless and wasteful expenditure incurred during the 2012/2013 financial year is R145 967 000 of which R125 212 000 relates to legal settlements by the department," he said.
The remaining R20 755 000 was made up of value of medication which expired, interest on late payments and penalties/interest relating to infrasture projects.
More than R5.7bn was reportedly marked as irregular expenditure for the 2012/2013 financial year.
Zwane said the amount was actually at just over R1.1bn and that it was currently under investigation.
A detailed report would be given to the standing committee, Zwane said.
This brought the amount of unauthorised, irregular, and fruitless and wasteful expenditure to more R1.6bn for the 2012/2013, according to Zwane.
