“The case is still under investigation and the suspect has not yet [been] charged,” Captain Thulani Zwane told Sapa.
The 51-year-old pastor had been arrested following the discovery of the dismembered corpse of four-year-old Kiki Ntuli in a plastic bag at the church at the weekend.
He had been reported missing on July 2.
As police searched for the rest of Ntuli’s body parts, they found a skull and a skeleton in the house of a woman in Ncotshane on Tuesday.
It was not yet clear if the skeleton was linked to the body parts found in the church.
Pongola residents however went on the rampage on Tuesday and torched the church and the woman’s house.
The pastor and the woman were not harmed in the incident.
Fifteen people were arrested on public violence charges and were scheduled the appear in the Ncotshane Magistrate’s Court on Thursday.
The court was however petrol-bombed on Wednesday night.
Zwane said it was suspected that the court had been set alight by angry community members regarding the arrest of the 15 people.
A case of arson had been opened.
Those arrested were expected to appear in the Pongola Magistrate’s Court on Friday, where they would apply for bail.
Two 17-year-old teenagers, who were part of the group, were released into their parents’ custody and told to attend the bail hearing.
National police commissioner Riah Phiyega on Thursday called for calm.
“We fully understand the community’s anger… but taking the law into one’s own hands, and committing crimes in the process, is not helpful at all. It only serves to prompt further police intervention and arrests,” Phiyega said in a statement.
She said the police would do all they could to ensure that justice was served.
The African National Congress and the National Freedom Party have condemned the violence in the area.
“The ANC… condemns in the strongest terms possible the ongoing destruction of private and public property in Pongola,” the party’s provincial treasurer Peggy Nkonyeni said in a statement.
The NFP said it was outraged by the killing and conveyed its condolences to the Ntuli family.
“The NFP says that the law must quickly take its course so that the doer of this satanic deed gets the heaviest sentence and rots in jail,” said NFP secretary general Nhlanhla Khubisa.
Meanwhile, another child was brutally murdered in Kutlwanong in the Free State.
According to post-mortem results, Karabo Nale was stabbed 99 times.
Her 23-year-old aunt, Nompucuko Mahamo, has been arrested for the murder after being found in possession of a blood-stained knife, two used candles and bloodied clothes.
She had last been seen heading to the shops with the toddler on Sunday.
The child’s body was discovered by a shepherd. A packet of Niknaks and sweets were found next to her body, said police.
Mahamo was scheduled to appear in the Odendaalsrus Magistrate’s Court on July 22 where she would apply for bail.