Coral shredded the ship's hull, causing it to leak 2-3 tons of fuel oil. Most of the oil was dispersed by a chemical spray and did little or no damage to the reef itself, but officials said Wednesday they believe some of it has begun to wash up on the beaches of a wildlife sanctuary.
The Great Barrier Reef is a World Heritage site because of its gleaming waters and environmental value as home to thousands of marine species. The accident occurred in the southern tip of the reef, which is not the main tourism hub.
The Australian Federal Police said the ship's captain and the chief officer on watch during the accident would appear in court Thursday.
"Investigations showed that the Shen Neng 1 failed to turn at a waypoint (a specific latitude and longitude) required by the intended course of the ship," the police said in a statement.
The 47-year-old shipmaster was charged with liability for a vessel causing damage in a marine park, an offense that carries a maximum 55,000 Australian dollar ($51,200) fine. The 44-year-old chief officer is charged with being in charge of the vessel when it caused the damage, and faces up to three years in prison and a fine of up to AU$220,000.
The police said officers executed a search warrant on the ship on Wednesday. It was not clear what they were looking for.
The ship's owners, Shenzen Energy Transport, said last week they were cooperating with the investigation.
Su Zengdong, the chief manager of TOSCO-KEYMAX, which is in charge of the vessel's technical management, said Wednesday that the company was "fully cooperating with the Australian side in the investigation and pollution control." He had no further comment.
The 755-foot (230-meter) ship was successfully lifted off the reef Monday after crews spent three days removing its fuel to lighten it. Salvage crews later towed it to an anchorage area near Great Keppel Island, 45 miles (70 kilometers) away.
Before it was removed, tides and currents repeatedly pushed the ship along the reef, cutting a scar 1.9 miles (3 kilometers) long and up to 820 feet (250 meters) wide into the coral.
Paint from the hull, used to prevent marine life from growing on it, was also smeared into the reef. Certain paints contain chemicals prevent growth, while others simply act as a barrier.
Experts are analyzing paint samples to determine if it is the more toxic variety.
"There is more damage to this reef than I have ever seen in any previous Great Barrier Reef groundings," Great Barrier Reef Marine Park Authority chief scientist David Wachenfeld said Tuesday. In some areas, "all marine life has been completely flattened and the structure of the shoal has been pulverized by the weight of the vessel," he added.
Globules of oil believed to be from the ship have washed ashore on North West Island, a turtle hatchery and bird sanctuary, said Adam Nicholson, a maritime safety spokesman for the northeastern state of Queensland.
Teams began Wednesday to clean up the globules, which were about an inch (3 centimeters) wide, and were scattered across about a half-mile (1 kilometer) of beach.