The warning came after three people were killed and two critically injured after being struck by lightning during a prayer session on Sunday afternoon.
The incident occurred during a flash storm in the suburban area of Kensington, Johannesburg, on a steep hill used as a prayer spot by the church.
The group was apparently taking part in a prayer service when lightning hit.
A member of the church, who did not want to be named, said she was still in shock as she also attended services on the hill.
"I'm really not in the right frame of mind to speak out right now. All I can say is that three lives were lost," she said.
She said she was not at the church service at the time but arrived soon after the lightning had struck. "I was called immediately after it happened and I went there."
She said the incident was a wake-up call for people to be cautious during the rainy period.
"This can happen anywhere. It really is important to take caution whether you are at home or on the street."
The injured church members are receiving treatment at Charlotte Maxeke Academic Hospital.
Weather service spokesperson Hannelee Doubell said when lightning strikes it always looks for the highest point.
"We will do an investigation and talk to the department of science and technology on what is the cause of the lightning, and if it only happened to the previously disadvantaged as I have never seen any white people being struck by lightning" said Dube.
True, it really happened . . .