In a Facebook post, self-proclaimed prophet Lethebo Rabalago claims a pesticide called Doom can heal people.
The company that produces Doom warned of the risks of spraying the substance, while a government commission urged anyone affected to lodge complaints.
But the pastor has defended his actions, telling the BBC he is using unconventional methods to heal people.
The country has seen a wave of practices where church members have been subjected to unorthodox rituals to receive healing.
In photos circulating on Facebook and Twitter, Mr Rabalago, who runs the Mount Zion General Assembly in the Limpopo province, is seen spraying the insecticide directly into the eyes and various body parts of his congregants.
He told the BBC’s Nomsa Maseko in Johannesburg that he had sprayed the face of one woman because she had an eye infection and claimed the woman was “just fine because she believed in the power of God”.
He also claims the spray can heal cancer and HIV.
“Doom is just a name, but when you speak to it to become a healing product, it does. People get healed and delivered through doom,” a post on the church’s Facebook account reads.
Testimonies of people who have supposedly been healed by Doom have also been posted on the Facebook page.
In another interview, , the pastor is heard saying: “The truth is, Doom can heal people in the right way.”