Docho Eshete was conducting the ceremony for about 80 people on Sunday morning at Lake Abaya in Arba Minch town's Merkeb Tabya district.
Residents and police told BBC Amharic a crocodile leapt from the water during the baptism and attacked him.
to another one. All of a sudden, a crocodile jumped out of the lake and grabbed the pastor," local resident Ketema Kairo told the BBC.
Despite huge efforts, fishermen and residents could not save pastor Docho, policeman Eiwnetu Kanko said.
They used fishing nets to prevent the crocodile from taking the pastor's body into the lake.