The increase in the number of large cargo ships in the area is devastating the communities of whales who gather there to breed, with large numbers killed or maimed by the boats or their propellers, according to the International Fund for Animal Welfare.
The report titled Collision Course said 11 large cargo ships pass through key humpback whale habitat in the Great Barrier Reef Marine Park every day.
This was expected to double by 2020 as coal-loading ports open to shipping. Most travel at 12 to 14 knots, and a whale struck at that speed would have a 70% chance of dying from its injuries, it said.
The report called for speed limits of 10 knots in whale breeding and nursing areas, which would bring the death rate from collisions down to three in 10, it said.
There is little data of current whale strikes by shipping. Matt Collis, marine campaign manager at IFAW, said speed restrictions in New Zealand had resulted in a sharp drop in collisions.
However getting statistics was difficult as people on a big ship would not even notice it had hit a whale, he said.
"Most whale strikes are reported by scientists on examination of stranded animals which have had their insides turned to mush by being hit by a boat", Collis told The Guardian.