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According to a report released by the office of the auditor-general, Limpopo accounted for most of the overall R167-million in wasteful expenditure across all the departments with R95.9-million.
This was attributed to purchases that were not used and interest on late payments.
Eastern Cape recorded R54-million in wasteful expenditure, which accounted mainly for "employees' salaries" .
Meisie Nkau, business executive in the auditor-general's office, said it was worrying that of the total amount in wasteful expenditure, prior to the auditor-general's own scrutiny, the national Department of Basic Education had only disclosed R37-million of the R167-million.
She said irregular and wasteful expenditure showed flaws in the provincial and national departments' ability to adequately control finances.
Nkau said considering the provinces spent between 90% and 99% of their allocated budgets, much more in service delivery should have been expected from them.
Of the targets set, only Gauteng and KwaZulu-Natal achieved over 80% of their targets. However, Limpopo only managed to achieve 10% of its planned goals and Eastern Cape achieved 35%.
Because Free State received a disclaimer from the auditor-general, its statements could not be verified for accuracy, said Nkau.
Unauthorised expenditure amounted to R1.4-billion, with KwaZulu-Natal accounting for R954-million, Eastern Cape for R297-million and Limpopo forR175-million.
Alongside the millions spent on compensation for employees, unfair and uncompetitive procurement processes were also red-flagged.
For supply chain management-related irregular expenditure, Eastern Cape topped the chart with R779-million, followed by Northern Cape with R380-million.