Emergency services began an extensive air and sea search for the 43-year-old on Monday after his family reported he had failed to return home at Glass House Mountains following a solo fishing trip.
His phone was recovered from the boat but the skipper, however, could not be found.
Sunshine Coast District Search and Rescue Coordinator Murray Lyons said the outcome was heartbreaking.
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“Despite our best efforts, we have been unable to locate the man and bring him home to his loved ones,” he said in a statement.
“We have liaised closely with his family and discussed the sad news regarding the likelihood of survival; they have asked for privacy during this difficult time.”
The man’s family thanked all the emergency service personnel, volunteers and the community for their contribution to the wide-scale search.