Docho Eshete was involved in a baptism ceremony for 80 people in Lake Abaya in Arba Minch.
Members of his church failed in attempts to save him.
Speaking to the BBC, local resident Ketema Kairo said: "He baptised the first person and he passed on to another one. All of a sudden, a crocodile jumped out of the lake and grabbed the pastor."
Those at the ceremony prevented the pastor's body being taken by the crocodile who escaped.
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