A 28-year-old pastor has been arrested for the murder of one of his followers allegedly committed in April despite police not being able to locate the body.

Pastor Henny Chabalala of the Liberty PHD Ministries in Siyandhani village in Giyani, Limpopo, was arrested on Thursday for the murder of his friend and neighbour Godfrey Pulasi. He appeared in the Modimolle magistrate's court on a charge of motor vehicle theft.

Pulasi, 31, was last seen alive on April 5 when he, Chabalala and two other friends left the village for Maputo in Mozambique to perform rituals for the church, police said.

Col Moatshe Ngoepe said Pulasi's remains were still missing but the man of the cloth is now facing a murder charge.

"The preliminary police investigations have revealed that the suspect was also in possession of the victim's cellphone and used it on several occasions.

"Even though the victim has not yet been found, the police have charged the suspect with murder, while the search operation for Pulasi and investigations as to what led to his disappearance are still ongoing," Ngoepe said.

"It is alleged that on April 5, the suspect and his two friends, joined by the victim, took a journey to Maputo on foot, apparently with the purpose of performing rituals for his church.