Andrew Heard, 69, set out to fish near Hinchinbrook Island on Thursday but didn't return, according to Queensland Police.
Investigators have since found human remains in the area and inside a 13.8-foot crocodile, police said Sunday.
The crocodile was caught and killed by the Queensland Department of Environment and Science (DES), which also killed a 10-foot crocodile as part of the investigation, the agency tweeted Monday.
"At this stage we can only confirm that we've found human remains in the first," Acting Inspector Andrew Cowie of Queensland Police said at a press conference Monday, explaining that the examination process has not been completed on the second crocodile.
Both animals were found in the area where Heard was believed to have been fishing, said Cowie, and the characteristics of the second crocodile are consistent with being involved in the incident.
"i believe that we've got the two crocodiles involved," he said.
Police found a small vessel with quite significant damage, said Cowie, who added that the investigation will now be passed on to the coroner.