The Shen Neng 1 was floated and taken from the damaged area of the reef Monday, after which officials said a scar nearly 2 miles long and about 300 yards wide was left by the craft on the fragile coral.
Additionally, scientists said paint scrapped from the ship's hull in the April 3 grounding was killing coral in the area. The craft also lost a substantial amount of fuel.
It will be some time before the full extent of the damage was determined, scientists said.
Given that the incident occurred in a location where such ship traffic is forbidden, Australian authorities promised to prosecute those responsible.
"It is still an absolute outrage that this vessel could've landed on the Great Barrier Reef," Australian Prime Minister Kevin Rudd said. "We will leave no stone unturned when it comes to finding out how that happened."