Police in Giyani, Limpopo, have arrested a 24-year-old pastor for allegedly raping a 16-year-old girl.

Police said the victim was allegedly raped by the arrested pastor and his colleague, who is still at large, between October 2018 and February 2019.

Police spokesperson Colonel Moatshe Ngoepe said the incidents were reported to the police who started with their investigations until the 24-year-old suspect was arrested.

"The second suspect was also identified but he has since disappeared after realising that he is being sought by the police. Preliminary police investigations revealed that the two suspects have allegedly raped the victim in separate incidents on different days and at several places," he said.

Provincial police commissioner Lieutenant-General Nneke Ledwaba condemned the ongoing sexual violence perpetrated against women and children, which are still occuring frequently in some parts of Limpopo.

"Members of the community, especially parents, are advised and encouraged to strengthen child safety at all times to prevent or avoid this type of incidents from occuring," he said.

The suspect is expected to appear in the Giyani magistrate's court on Friday, while manhunt for the second suspect, who is in his 30s, is still underway, Ledwaba said.