It appears the boat was involved in some kind of collision at high speed, with "significant damage to the front, below the water line", Queensland Police said in a statement.
Shaun Halson from Queensland Water Police told reporters that the area is characterised by "lots of small, rocky islands and submerged objects".
While the weather was fine last night, the sky was darkened by thick smoke from bushfires.
"While (the collision) was at speed, there's nothing to suggest that speed was excessive," he said.
The two men appear to have died in the collision, initial inquiries indicate. The pair were the only passengers on board.
"A passing sailing vessel had observed a motor vessel, which appeared to be in difficulty but they were unable to assist at that time."
The Sailfish 3000, a six-metre aluminium catamaran, suffered significant damage to the front, below the water line, police said.
Investigations are continuing.
