An 80-strong congregation looked on in horror as the reptile struck at Docho Eshete, a protestant clergyman in the town of Arba Minch, while he conducted a mass baptism in the shallows of Lake Abaya on Sunday.
The pastor, identified as Docho Eshete, died after being bitten on his legs, back and hands.
The incident came a month after a crocodile in Zimbabwe ripped off the arm of local resident Zanele Ndlovu, 25, five days before she was due to marriy her British fiancé, Jamie Fox, 27.
Fishermen and those who attended the ceremony are said to have tried to save the pastor.
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A baptism in Ethiopia has gone horribly wrong, with a crocodile attacking and killing the pastor during a waterside service.
The crocodile escaped as the group used fishing nets to prevent it from taking the pastor's lifeless body.
The Crocodile Specialist Group estimates that Nile crocodiles are responsible for more than 300 attacks in Africa each year.