The City of Tshwane will issue instructions to force Pastor Shepherd Bushiri's church to comply with security regulations after it found that they were flouted.
This follows the recent stampede at the Enlightened Christian Gathering Church that claimed the lives of three women and injured many congregants.
The incident occurred while people were trying to reach shelter during a heavy thunderstorm.
The church has been charged with defeating the ends of justice over the way it handled the incident.
The city has since conducted an inspection and found a number of issues that didn't comply with safety standards.
Meanwhile, the Enlightened Christian Gathering Church says has described last month's deadly event at the Tshwane Events Centre as a natural disaster which was simply out of its control.
The church says that while it deeply regrets the deaths of three of its members, the events were simply out of its control.
Spokesperson Maynard Manyowa says the church has since launched an internal investigation into what happened.
“But in the face of a pounding storm, panic and what we perceive perhaps a natural disaster, we were overwhelmed.”
At a media briefing in Pretoria on Friday, Manyowa also said Bushiri was not at fault.
Manyowa said the church was registered in SA and owned by South Africans.
"The event that transpired was not a stampede within Shepherd Bushiri's home, but at a premises which is rented and utilised by the Enlightened Christian Gathering church, which he is a part of."
Earlier on Friday, a site inspection by the Tshwane's fire and emergency services department revealed that the venue was non-compliant regarding safety issues.
Manyowa says the church has since launched an internal investigation into what happened.
“Only the truth can help us improve the robustness of our systems and limit the last possible percentage point, the possibility of any further tragedies.”
The church says that the leader of its Tshwane branch has since been suspended pending the outcome of the probe.