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Mthokozisi Mdanda went missing on Sunday last week at about 3.30pm. His father said he had spoken to him just after 3pm when he drove past in his taxi.
Themba Sibeko, 47, told Sowetan on Monday that he discovered his son's decomposing body on Saturday night after watching the Soweto derby between Kaizer Chiefs and Pirates.
He claimed to have found him in a rubbish bin used to store old clothes, located in the far corner of his garage.
Sibeko said he had gone to the garage to look for curtains he had washed.
"I went into the garage and was struck by the odd smell. I started calling out Mthoko, Mthoko ... I lifted a mattress and looked behind some things before lifting the rubbish bin lid. Oh, seeing my son like that ... he was my boy," Sibeko had earlier said.
But Soweto police spokesman Warrant Officer Kay Makhubele said sniffer dogs and forensic experts linked the father to the possible murder.
"We have changed the inquest docket to murder. The suspect we arrested is the father (of the child).
"Yesterday we reconstructed the scene where the body was found and forensic experts and sniffer digs were called in.
"Traces of blood were found in the yard, next to the bin (in which the boy was stuffed) and on the father's clothing ..."
Sibeko is expected to appear in the Protea Magistrate's Court in Soweto tomorrow.