The search continued on Friday with police vessels, State Emergency Service volunteers, the Ingham Coast Guard and fishermen.
The Department of Environment and Science said two wildlife teams were sent to the area to help police and more personnel would be deployed.
“Departmental experts on the ground have examined the vessel and determined that it is highly likely that a crocodile is involved, however the exact circumstances and sequence of events remain unknown,” the DES statement said.
“A search for the animal is now under way. An incident control room has been established in Townsville. Our thoughts are with the family of the missing man at this time.”
Police Inspector Andrew Cowie said the man was an experienced fisherman and his disappearance was a “significant concern”.
The search area was large around Hinchinbrook and despite rain restricting the search efforts, those involved were focusing on the coastline, as well as local rivers and creeks.
Inspector Cowie said the man had only taken a radio with him, no life jacket or EPIRB, but the search operation would continue “as long as there is a chance that he is alive”.