Witnesses say a crocodile then launched itself from the water during one of the baptisms and attacked the pastor who died after receiving bite marks to his legs, back and hands.
Crocodiles are found in freshwater habitats like rivers and lakes.
Some 80 people set to be baptized at a lake in southern Ethiopia instead watched as their pastor was killed by a crocodile Sunday.
The crocodile escaped as the group used fishing nets to prevent it from taking the pastor's lifeless body.
"He baptized the first person and he passed on to another one", a local resident told the BBC.
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Residents and fishermen made a huge effort to save Pastor Docho but were unsuccessful, policeman Eiwnetu Kanko said.
Ethiopian news outlet Borkena.com said members of the church were left devastated by the gruesome attack and reported it widely on social media.
The "reddish-brown" water also makes it hard to spot crocodiles in the vicinity, per the Telegraph.
The crocodile was not captured.
Crocodile attacks are common in Africa, the paper reported, with numerous victims being women washing clothes.