The South African Police Service has opened a case of defeating the ends of justice against Shepherd Bushiri's Enlightened Christian Gathering (ECG) church.
This followed the deaths of three women during a stampede on Friday night.
Nine other people were injured when in the crush as people attending a church event at the Pretoria Show Grounds jostled for cover when it began to rain.
Police spokesperson, Captain Augustine Selepe, said the charge was laid because the matter was not reported to the police and that the bodies of the victims were removed to a private mortuary.
The victims have not yet been identified.
African News Agency (ANA)