"All the oil has now been cleaned," a spokesman for Maritime Safety Queensland told AAP.
But the agency's general manager, Patrick Quirk, said a light oily sheen may still be visible on the river for several hours.
"This is expected to be broken up by natural water action and does not pose a risk to the environment," Mr Quirk said in a statement.
All major shipping was stopped by the harbourmaster for the duration of the clean-up and normal operations resumed at 2pm.
"This is good result for our marine pollution response team, who have had extensive experience in these types of clean-up operations," Mr Quirk said.
Investigators have now boarded the ship and are taking oil samples to further identify its source.
They will also investigate the scale of the spill.
The Australian Maritime Safety Authority has ordered the boat not to leave port.