The Australian Federal Police said the ship's master, a 47-year-old man, has been charged with liability for a vessel which caused damage, and the chief officer-on-watch, a 44-year-old man, will face an offence of being the person in charge of a vessel that caused damage to the Great Barrier Reef Marine Park.
Both Chinese men were arrested on board the Shen Neng 1 yesterday afternoon and spent the night in custody.
They are due to appear in the Gladstone Magistrates Court today.
Maritime Safety Queensland said the Shen Neng 1 leaked up to four tonnes of fuel oil onto the reef when it ran aground on Douglas Shoal, off Rockhampton, on April 3.
Oil has washed up on two islands, including an important turtle and seabird rookery.
Marine scientists say the ship has gouged a channel, about three kilometres long and 250 metres wide, in the marine park.
The Australian Transport Safety Bureau will release its preliminary report into the grounding today in Canberra.
The Australian Maritime Safety Authority was due to hand the federal government its report, also today.
It is expected to recommend extending a Vessel Tracking System, similar to air traffic control, for the entire length of the reef.
The tracking system currently runs from the Torres Strait to just south of Mackay.