Emergency services were called to Hull River Heads boat ramp, about 160km south of Cairns in far north Queensland, shortly before noon on Sunday.
It followed reports the man had been attacked by a shark at Kennedy Shoal, a submerged reef some distance offshore from Tully Heads.
Queensland Police Inspector Elaine Burns said the 39-year-old was attacked while in the water with another person, who retrieved him and helped bring him back onboard a private vessel.
The vessel, understood to be about seven metres long, arrived back at the boat ramp about 1pm, where the man was declared dead.
He was one of four passengers on the vessel, though it's not clear whether he was known to them.
"This is a tragic incident for everyone involved, and we will continue to provide support to the family and those who were on board with him," Insp Burns told reporters on Sunday.
Asked about the condition of witnesses, Insp Burns said they would likely be traumatised.
"That's quite a terrifying thing to see happen right in front of you," she said.
Police said investigators would work with the Department of Environment and Science as part of efforts to identify the shark species involved.
Sunday's death comes just over a week since father-of-two Steven "Mattas" Mattaboni died in a shark attack in Western Australia.
Mr Mattaboni was diving at Horseshoe Reef near Rottnest Island on May 16 when attacked.
Kennedy Shoal, where Sunday's fatal attack occurred, is popular for recreational fishing and diving.
Commercial fishing operator Gererd Pike was working about six nautical miles away when the attack occurred.
He said sharks had become increasingly aggressive and numerous along much of the coastline due to restrictions on catching large sharks.
"We had at least six sharks tearing into a mackerel at one point," Mr Pike told AAP.
"They're constantly active on the reef and some days it's beyond the point of fishing."
Mr Pike said local fishermen and residents were shocked by news of the fatal attack.
"I've had some gnarly calls on that reef in the past, definitely in the last 20 years," he said.
"It's becoming a real problem."
In October, a 14-year-old boy was critically injured in a shark attack near Thursday Island, in far north Queensland.
He was bitten on the stomach while fishing with friends near Cook Esplanade, off the nation's northernmost tip.
In February 2025, 17-year-old Charlize Zmuda died after being bitten by a shark while swimming off Woorim Beach at Bribie Island, in Queensland's south.
It follows a spate of fatal shark attacks along NSW's coast.
Schoolboy Nico Antic, 13, died a week after being bitten on his legs near a popular swimming spot at Vaucluse, in Sydney's east, in January.
Swiss tourist Livia Mulheim, 25, was killed by a shark in November while swimming at a Kylies Beach on NSW's mid-north coast.
Surfer Mercury Psillakis, 57, was fatally bitten by a shark at Sydney's Long Reef beach in September.
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