A massive land, sea and air search on Wednesday has failed to find a man who went missing off the coast of Cairns in Far North Queensland on Tuesday.

Police said the 55-year-old man launched his 5.6-metre boat alone from Mourilyan Harbour, south of Cairns, around 6:00am on Tuesday.

The man's relatives raised the alarm at 4:00pm on Tuesday when he failed to return from the trip and a search and rescue operation was initiated.

Kayakers found the man's boat drifting in the mouth of the Johnstone River — a known crocodile habitat — around 6:40pm before the search operation was suspended overnight.

Inspector Denis Fitzpatrick said five helicopters, two planes, a water police vessel and a volunteer coastguard vessel were searching for the man in an area of more than 450-square kilometres off the coast.

"We believe he was an experienced fisherman but we have some information that he hasn't been fishing or used this particular vessel for a couple of years," he said.

"We can't confirm he's made it to the reef [but] he had bait on board and foodstuffs and certainly his intention was to go directly out through the Barnard Islands to go fishing.

"Nothing on board the boat would indicate that he had done any fishing at the time [of his disappearance].

"We've got no idea what's happened other than he's not on the vessel … so we're searching, suspecting that he's fallen into the water."

Inspector Fitzpatrick appealed to other boat users who were in the area yesterday who may have seen the man or his white Bar Crusher vessel to contact police.

The search is expected to resume at first light on Thursday.