"They have found significant scarring and coral damage, they've also found quite a lot of anti-fouling [paint] spread across the reef," Reichelt told ABC public radio.
He said the paint was a particular concern "because it's designed to be toxic and stop things growing on ships".
"We've already seen observations where anti-fouling paint that's been scraped off onto the reef is killing corals in its vicinity."
Late on Monday night salvage teams managed to refloat the bulk carrier by pumping compressed air into its hull and pulling the vessel free using tugboats.
"We're actually not out of the woods on this yet. Until this ship is repaired and out of the Great Barrier Reef, none of us will really rest easy"
Rachel Nolan, Queensland state transport minister
Travelling at full speed and in broad daylight the Shen Neng 1 struck the reef after straying off a recognised shipping lane.
The carrier leaked two tonnes of heavy fuel oil onto the reef when it ran aground, but crews managed to pump out most of the 970 tonnes before refloating it.
Divers are due to assess the damage to the ship, which has been towed to an area east of Great Keppel Island.
The vessel, still carrying 68,000 tonnes of coal, had been grinding across a shoal, creating plumes of coral dust in the water.
"We're actually not out of the woods on this yet," Rachel Nolan, the Queensland state transport minister, told ABC.
"Until this ship is repaired and out of the Great Barrier Reef, none of us will really rest easy."
Australian officials have accused the ship's crew of taking an illegal route through the reef, listed as a World Heritage site, promising to probe claims that ships were taking a short-cut.
The government said it would be "throwing the book" at those responsible, adding that it will consider extending a ship-tracking system which controls vessels moving around other parts of the reef and review shipping regulations.
Environmental laws bar shipping in the area in order to protect what is the world's largest coral reef.
Days after the Shen Neng 1 incident, three crew members from a Panama-flagged bulk carrier were charged with illegally entering a restricted part of the reef, and are due to reappear in court in the northeastern city of Townsville on Friday.
South Korean Gang Chun Han, 63, and Vietnam's Tran Tan Thanh and Nguyen Van Sang face maximum fines of A$225,000 ($205,000), after allegedly taking the MV Mimosa through the reef.
The Great Barrier Reef sprawls along some 3,000 kilometres of Australia coast, and is home to thousands of marine species and a major tourist attraction.
The reef, which is visible from space and is one of the world's foremost ecological treasures, has already come under pressure from rising sea temperatures and pollution.