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Hundreds of boxes of medication were found dumped outside a village near Mthatha on Friday afternoon.
Eastern Cape health department spokesperson, Sizwe Kupelo says the boxes were found by police, and were from the Mthatha Medical Depot.
He says the department will launch an urgent probe, and will start with the managers at the depot and investigate how it happened.
Kupelo says a security company is also responsible for looking after the medication while it is being transported.
He says the health department had been accused of poor service delivery, and "elements" in the province are trying to ruin its reputation.