The Great Barrier Reef Marine Park Authority (GBRMPA) says the Shen Neng 1 has left a column of damage about one kilometre long.
It says toxic anti-fouling paint from the hull is killing coral around Douglas Shoal, off Rockhampton, where the ship ran aground in a restricted part of the marine park on April 3.
The ship was finally refloated on Monday evening and is now anchored in safe waters off Great Keppel island.
Marine park authority chairman Russell Reichelt said the clean up will be one of the biggest of its type and damage is significant.
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"It didn't just go aground and stop," he told the ABC, adding it moved about a kilometre after running into the shoal.
He said an initial inspection had found significant scarring and coral damage, and a lot of anti-fouling paint on the reef.
"The paint that's scraped off (onto) the reef is killing corals in its vicinity," he said.
It could be weeks before the full extent of the damage was known, he said.
For many of the nine days the ship was stranded, footage showed a white plume around the ship - evidence that the hull was crushing coral as it moved with the wind and swell.
A team of marine scientists is at the scene of the grounding to carry out a full assessment of environmental damage.
That process is being led by the marine park authority, with help from the Queensland environment department and the Australian Institute of Marine Science.
Federal environment minister Peter Garrett said he'd asked the marine park authority for a thorough review of the site.
"Ship groundings can result in significant localised damage to habitats. Groundings such as this often leave grounding scars in the reef substrate where the coral is crushed and compacted," he said in a statement.
The inspection team will document damage from the point where the ship ran aground, across part of the shoal to the site where it ended up.
They will gather photographic and video evidence of the damage.
"I anticipate the assessment and monitoring of this site and the other environmental impacts of this grounding are likely to be ongoing," Mr Garrett said.
"The Scientific Advisory Panel I asked GBRMPA to establish earlier this month, will review the information from the environmental inspection and advise on the next steps."
