The commission has been trying to contact Pastor Penuel Mnguni for six months.
He was last seen when his Soshanguve tent church was burnt down in August.
Mnguni is one of several religious leaders being asked to account for his church's practices.
The commission wants him to explain why he allegedly made congregants eat rats and snakes.
The Chapter nine institutions are investigating the alleged commercialisation of religion and the abuse of beliefs.
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