"The man had been fishing with family and friends on Darwin Harbour when he was struck in his chest by a large fish," Northern Territory police said.
The party returned the man to shore, where paramedics administered CPR.
"Sadly the man the man passed away," police said.
"This appears to be a freak incident which is hugely distressing for the people in the boat and other family and friends of the man."
It was not immediately clear what type of fish was involved.
In a similar incident nearby in 2018, a woman narrowly survived when she was fishing and her throat was slashed by a mackerel.