Kevin Darmody, 65, was last seen at Kennedy's Bend - a well-known saltwater crocodile habitat in a remote part of northern Queensland - on Saturday.
After a two-day search of the area, police euthanised two large crocodiles and found human body parts.
Police said it was a "tragic ending" for Mr Darmody. A formal identification process will be carried out.
Mr Darmody was an experienced fisherman and a well-known member of the community in Cape York.
