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A tugboat arrives to help monitor the 230-metre bulk coal carrier Shen Neng I, which ran aground on the Great Barrier Reef on Saturday. ((Maritime Safety Queensland/Reuters))

Australia's prime minister is calling the grounding of a foreign ship on the Great Barrier Reef "outrageous" and says his country may have to increase shipping restrictions to prevent other ships from doing the same.

"Here you have this massive boat, this massive ship, 12 kilometres off course, broad daylight, in the middle of the Great Barrier Reef," Kevin Rudd said Wednesday, referring to the Shen Neng 1, a Chinese vessel that ran aground late Saturday afternoon on a shoal northeast of Gladstone.

It has so far leaked three to four tonnes of heavy fuel oil into the pristine waters surrounding it. The fuel has been dispersed by chemicals.

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A worker on the Shen Neng 1 checks equipment as the ship sits aground on the Great Barrier Reef near Great Keppel Island, on Wednesday. ((Maritime Safety Queensland/Associated Press))

Australia will conduct a thorough investigation into "how the hell this happened," Rudd told reporters. "And if we need to also look at other measures for the future including a wider use of pilotage and the wider use of the vessel tracking system that applies in the northern parts of the reef, then we will," he vowed.

The government has already dispatched a boat from the Australia Maritime Safety Authority to put a float around the grounded vessel to keep it stable and prevent further spillage.

Bunkering ships were also sent to transfer the coal-carrying ship's remaining 946 or so tonnes of heavy fuel oil from tanks that were damaged in the grounding to more secure tanks to "minimize the risk of further oil spilling into the water," according to Patrick Quirk, general manager of Maritime Safety Queensland.

'The most significant immediate damage was to the reef structure itself where the ship plowed into it.' —Peter Harrison, Southern Cross University

"Despite the scale, this is actually a delicate operation and we won't be rushing it," Quirk said in a statement. "Every bit of oil in the water risks the marine environment and the shoreline."

Eventually, maritime officials hope to remove enough of the ship's cargo to be able to refloat it and remove it from the reef area.

Damage already done: researcher

Reef researcher Peter Harrison said some physical and chemical damage has already been done.

"The most significant immediate damage was to the reef structure itself where the ship plowed into it," said Harrison, director of marine studies at Australia's Southern Cross University.

"That would have killed some corals and some of the other reef organisms in the vicinity," Harrison said. "The subsequent danger has been from the leakage of oil."

Oil is toxic to corals, Harrison said, and can lead to bleaching and eventual death. Dispersing the oil by chemicals is not the ideal solution, as the dispersants are also toxic to corals if they are not washed away quickly enough, but was better than letting the oil seep into the corals and sand.

Maritime Safety Queensland said the vessel was not within the preferred shipping channel through the reef, but was on an acknowledged alternate route — although obviously off course — when it ran aground.

Previous reports had suggested the ship was on an illegal shortcut through the Great Barrier Reef Marine Park.