Thami Tukane, 48, was reported missing on Sunday after his vehicle was spotted by a family friend last Saturday. It was left abandoned next to the N8 road between Bloemfontein and Thaba Nchu in the Free State.
When his family realised that he had gone missing for four days they called in the police, who in turn referred the case to the Hawks in Bloemfontein.
Tukane's body was found in Ladybrand on Monday afternoon.
According to police spokeswoman Thandi Mbambo it was unclear what had happened leading to his disappearance last week.
She said when his car was found abandoned nothing sinister was discovered.
"No visible signs of injuries were found on his body and his vehicle was not tampered with," she said.
She said a postmortem would be conducted to determine the exact cause of Tukane's death.
She said an inquest had been registered for further investigation.
His death follows that of Naledi local municipality mayor Motlatsi Motloi, who was shot dead in the area in May 2010.
Municipal employees Caroline Mokgothu and her husband James were sentenced to life imprisonment for arranging the killing of Motloi, 32.
He was shot dead in front of his house in Wepener, Free State, on May 3.
Naledi municipality has been plagued by squabbles between councillors, officials and workers since 2006.