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Shembe had headed one of the four factions of the church since 1933.
Church leaders and family members did not reveal what Shembe had suffered from as his illness had been kept under wraps.
As his body was removed from the church's headquarters in Ebuhleni, Durban, to the mortuary, throngs of worshippers and the general public of Inanda, north of Durban, broke down and wept.
Despite rivalry between the church's Ebuhleni faction and the eKuphakameni faction under the leadership of Inkosi Vukile Shembe, Vukile's spokesperson Edward Ximba expressed sadness.
"We hope that church members will be able to handle the situation and seek God's divinity as they mourn the death of their leader," Ximba said.
According to the spokesperson, Vukile had also sent his condolences to worshippers at Ebuhleni.
"Yes, we have differences but were not enemies," Ximba added.
Vimbeni Shembe's faction of the church has more than one million followers, most of whom are Zulus.
The church has four factions, all claiming to be the legitimate leaders of the Shembe church.
The charismatic church, founded in 1910, is estimated to have assets of over R100million.
The four factions have taken each other to court over who is the legitimate heir to church founder prophet Isaiah Shembe.
Turmoil was sparked by the death of the prophet's successor, Bishop Galilee Shembe, in 1976.
Two factions surfaced - led by the bishop's brother Amos Shembe and the bishop's son Londa Shembe.
The church is now split into the Ebuhleni faction, which was led by Amos's son Vimbeni Shembe, regarded as the wealthiest and most powerful.
The others are the Ekuphakameni, led by Londa's son Vukile Shembe; Ginyezinye, led by the bishop's grandson Sizwe Shembe; and a Gauteng faction, led by another of the bishop's grandsons, Phakama Shembe.