In an Australian first, coal could be loaded between ships in the middle of the Great Barrier Reef.
Environmentalists are concerned that ships could crash into each other, spewing coal into world heritage-listed waters, as the activity disturbs fisheries and turtles.
Mitchell Ports has applied to the federal Department of Environment for permission to send barges into the Great Barrier Reef Marine Park.
Instead of docking at a land-based port, ships would anchor offshore, above a sand bed, as cranes on a barge transfers coal from a smaller ship to a larger vessel.
Mitchell's subsidiary company, Hay Port Exports, is applying to build a new barging and trans-shipping terminal at Hay Point, south of Mackay in central Queensland.
But it admits its Bowen Basin Terminal plan, which will handle up to 15 million tonnes of coal a year, could affect near threatened migratory species, such as the irrawaddy and indo pacific humpback dolphins.
"Although it is likely to be minimal, the project could impact on listed, threatened and migratory species," it said in its application.
The Australian Marine Conservation Society said the transfer of coal between ships in open, choppy waters in posed risks to sea life, especially if there was an accident.
"We could see boats crash into each other. We could see coal spewing into reef waters," campaigner Felicity Wishart told AAP, adding light pollution and noise could affect spawning fisheries and turtles.
"We don't think a marine park is a place where you should be dredging, dumping or transferring coal from ship to ship."
Mitchell Ports, however, argues its trans-shipping proposal minimised the need for sea bed dredging, which occurs when a land-based port is expanded.
Ms Wishart said the practice of ship-to-ship transfers occurred in Indonesia but had not been done in Australia before.
Mitchell Ports executive director Ben King, who is managing the Hay Port project, admitted there were risks with the proposal, but said it would use European technology.
"There's always the potential for accidents and we have to make sure that ... our engineering comes up with a suitable risk profile where we have safeguards," he told AAP, adding this type of trans-shipping was carried out in Italy and the Netherlands.
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