With a huge coal-carrying ship stuck on the Great Barrier Reef and leaking oil, the Australian Conservation Foundation has called for export ships to use alternative routes that avoid the world renowned marine icon.

The ship, the Shen Neng 1, is loaded with 65,000 tonnes of coal and 975 tonnes of heavy fuel oil. Some of the fuel has already leaked into the waters of the Great Barrier Reef Marine Park.

The ship ran aground 70 kilometres east of Great Keppel Island.

It was at least 15 nautical miles off course and appears to have been taking a short cut through the reef.

ACF's Healthy Oceans Campaign Coordinator Chris Smyth said the oil spill would have a detrimental effect on the local area's pristine coral reefs and the marine life that use them including dolphins, dugongs, rays, turtles, clown fish and numerous other reef species.

"The stuck ship and the fuel oil will be doing damage to the area directly around the ship, but we really don't know what effect the load of coal might have on the reef if the ship breaks up," he said.

"What is going to happen to the Great Barrier Reef if it's smothered in coal?

"We urge the Queensland government and the Federal Government to look at doing research work on what effect coal, LNG and oil will have on Great Barrier Reef marine life."

He said the clash between environmental and industrial interests was likely to intensify as governments pursued a coal and gas ‘resources boom' and large shipping traffic rapidly increased.

Developing more ports will also impact on coastal and marine environments.

"This upsetting incident raises big questions about the lack of effective regulations around the transporting of coal and gas out of Queensland ports and through state and Commonwealth waters," he said.

"In the short-term state and federal governments must extend the surveillance of the Vessel Traffic System to the Gladstone-Rockhampton region. They must also work to ensure local pilots who know the area well are aboard these vessels in state and Commonwealth waters.

"The Government must also look at establishing alternative shipping routes for the bulk carriers that avoid the Great Barrier Reef, otherwise these sorts of accidents are going to keep happening."

"State and federal governments should enforce very heavy penalties for companies that disregard environmental and safety requirements.

"The shipping company concerned must take full responsibility for the cost of the clean-up," he said.

Mandatory local pilotage and alternative routes will require the agreement of international maritime authorities. But the Great Barrier Reef is a World Heritage Area, an international icon that the international shipping community should recognise as requiring special care.