The slaughter was in retaliation for a local man thought to have been killed by one animal from the site.
Officials and police said they were not able to stop the attack and may now press charges.
The killing of a protected species is a crime that carries a fine or imprisonment in Indonesia.
The local villager was killed on Friday morning while gathering vegetables on the crocodile farm's breeding sanctuary.
"An employee heard someone screaming for help, quickly went there and saw a crocodile attacking someone," the head of Indonesia's Natural Resources Conservation Agency in West Papua said.
After the funeral on Saturday, several hundred angry locals went to the sanctuary, armed with knives, shovels, hammers and clubs.
Local media cite officials saying the mob first attacked the office of the crocodile farm and then went on to slaughter all 292 reptiles at the sanctuary.
The farm was operating on a licence to breed protected saltwater and New Guinea crocodiles both for preservation and to harvest some of the animals.
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