The research ship is currently steaming south, on its way to the grounding site. The damaged coal carrier was moved to safe anchorage on Monday night, making the grounding site on the Great Barrier Reef accessible for investigation by the AIMS team.

The team will assess the scale and severity of the physical damage of the grounding; as well as the level of contamination from anti-foulant paint.

The AIMS cruise leader, Dr Andrew Negri said a multi-beam sonar would be used to map the sea floor to quantify physical damage to the structure of the reef.

"This instrument can resolve the seabed to less than 10 centimetres, which means it will accurately record the damage caused by the ship’s hull," he said.

Dr Negri said marine scientists would be diving with video cameras to take footage of the impacts on reef organisms such as corals, sponges and algae.

"In the areas that are too deep for divers, we have specialised cameras that can be towed by the ship," he said.

Dr Negri said the hulls of most large vessels are coated with an anti-fouling paint to reduce the growth of algae and barnacles.

"This paint usually contains toxic chemicals, including heavy metals and/or herbicides and if a ship is grounded, it usually scrapes onto the reef," he said.

Samples of the sediments will be taken for analysis to provide the Great Barrier Reef Marine Park Authority with a rapid baseline contamination assessment of the site.

Dr Negri said previous ship groundings had contaminated up to one hectare of the reef. Movement of the Shen Neng 1 since it was first grounded on Easter Saturday, means the area of physical damage and contamination may be much larger.

The Great Barrier Reef Marine Park Authority, James Cook University and Queensland Parks and Wildlife Service  will be providing support to the AIMS team during the investigation, which is expected to take about four days.