Chinese coal carrier Shen Neng 1 has now been refloated and towed to safe anchorage, but it could have left behind lasting damage on the Great Barrier Reef.
The ship gouged a furrow 3km long and 250m wide on the Douglas Shoal in the nine days it was stranded there, authorities said.
The major initial impact on the reef was that caused by the 100,000-tonne ship itself, as it rolled around on the coral for several days.
Authorities were also investigating whether oil found on North West Island, a bird rookery and turtle nesting site 10 nautical miles south of Douglas Shoal, came from the Chinese ship.
Scientists yesterday got their first good look at the reef since the bulk carrier was floated free on Monday night's high tide after being grounded off Gladstone on Easter Saturday.
Great Barrier Reef Marine Park Authority chief scientist David Wachenfeld said the damage to Douglas Shoal was the worst by a ship to any part of the Great Barrier Reef.
"This vessel did not make an impact in one place and rest there and then was pulled off," he said.
The coal carrier hit the reef at low tide but the next high tide was not enough to float it off, and for days the vessel moved around, buffeted by currents and winds.
Maritime Safety Queensland spokesman Patrick Quirk says the Shen Neng 1 lost oil twice on its initial grounding on Douglas Shoal, east of Rockhampton.
"We had another small spill on the Saturday afternoon last and it is quite possible that it is that oil [from the Seng Neng 1]," he said.
"We had aircraft out searching but aircraft can't pick up every drop of oil in the ocean, unfortunately."
Quirk says North West Island is the second largest coral cay on the reef and is home to key nesting grounds for seabirds and turtles.
"The place is very sensitive - it is one of the most sensitive areas of the southern area of the Great Barrier Reef," he said.
"It is world famous for its bird nesting and its turtle rookeries. We understand there are baby turtles being hatched at the moment and our concern is to protect the wildlife.
"[The oil] hasn't come ashore in large globules or carpets - our advice from the rangers on the island is it is at the top of the tide line in patches and that gives us some comfort.
"But we will need to get our specialist beach clean-up experts and they will report to us immediately what's there and if needed we will fly out more people."
Capricorn Conservation Council spokesman Ian Herbert says the pollution of North West Island is tragic.
"It's habitat for a huge variety of marine life - turtle hatchlings are there at the moment, nesting birds," he said.
"Any damage to North West Island is really quite a tragedy - we're upset that it has happened, as are all Queenslanders.
"For people to say 'they get the boom nets out just to capture all the oil' - it's not as easy as that.
"As you see from aerial photos, the oil floats on water and spreads rapidly quite widely, so it's quite to be expected that there will be some escape of oil."
Federal Environment Minister Peter Garrett says nearby islands may also have been contaminated.
Mr Garrett has told ABC Radio's AM program that Tryon Island is also environmentally sensitive.
"I'm very, very concerned but also aware that we are focusing on those places which have got high environmental values and that the clean-up will take place as quickly and effectively as it can," he said.
"I'm certainly very concerned that some of the neighbouring islands there like Tryon Island might also have been contaminated and so those islands of course will also be investigated as a matter of course."
However a major concern yesterday was the possible impact of anti-fouling paint from the ship, which has been smeared across the coral. Samples of the paint will be analysed over the next few days, and if -- as is likely -- they contain chemicals, there could be considerable long-term damage to the reef.
Even if the paint is non-chemical, the best possible outcome for the reef is that it will be 10 to 20 years before it returns to the state it was in before being hit by the Shen Neng 1.
Chief scientist David Wachenfeld said, "Everywhere we have been so far we have found paint. The majority of the impacted area has paint on it.
"That paint is quite likely to have heavy metals in it. That would really put a much longer timeframe on recovery because that paint would be stopping any plants and animals from recolonising."
Dr Wachenfeld said the shoal supported a variety of marine plant and animal life. "They would have been pulverised under the ship but they're not going to leave behind any observable trace," he said. "The paint that is there is smeared and is on the coral. This was not a gentle process -- you could imagine the impact of a ship of 100,000 tonnes pushing down on the reef, and the paint has been pressed on to the reef itself."
Anti-fouling paint is used on most commercial ships to keep off barnacles and other sea life that can slow down the vessel.
The Queensland government is urging that the vessel tracking system used in the northern part of the Great Barrier Reef be extended to the waters off Gladstone where the Shen Neng 1 ran aground. The federal government is expected to endorse the calls
The only solace perhaps is that the spill on the Great Barrier Reef island is not as bad as the massive spill that polluted south-east Queensland beaches last year.
Last March, a cargo ship leaked more than 270,000 litres of oil, prompting a clean-up from Moreton Island to the Sunshine Coast.