The Federal Court has heard up to one-and-a-half tonnes of toxic paint may have scraped off a grounded Chinese coal carrier into the Great Barrier Reef off the central Queensland coast in 2010.

A trial over the grounding of the Shen Neng One began in Brisbane today to determine who should pay to fix damage to Douglas Shoal, which the ship was stuck on for nine days before it was re-floated.

The 225-metre long carrier carved a 2.2 kilometre-long, 400,000-square-metre scar in and around the shoal, about 120 kilometres east of Rockhampton, which was the largest known damage to the Great Barrier Reef caused by a ship.

The grounding also damaged one of the ship's fuel tanks, which left a four-kilometre-long trail of heavy fuel oil.

The Commonwealth sought $120 million in remediation costs from the ship's owner, Shenzhen Energy Transport Co, or alternatively wanted the company to fix the damage to the shoal.

The court heard hundreds of kilograms of paint flakes containing the highly-toxic anti-fouling agent, tributyltin, had contaminated an estimated 112 hectares of shoal.

The Commonwealth said the compound was lethal to marine life and banned 20 years ago, but older vessels were allowed to continue operating with a top-coat to prevent the poison from leaching into water.

However, barrister Martin Scott, acting for the Commonwealth said between 750 kilograms and 1.5 tonnes of paint flakes were estimated to have scraped off the vessel into the water, and they had to be removed.

"The poison, the contaminant in a flake, will be there as long as the flake is there," he said.

"Not all of these flakes are just sitting on the surface, some of them have become mixed into the sediment for example."

Lawyers for the ship's owner disputed liability, saying the ship's chief officer, who was employed by an independent company, was to blame for the grounding.

The ship had veered more than 10 kilometres outside the shipping lane.

In 2012, the ship’s chief officer, Xuegang Wang, was sentenced to 18 months in jail over the incident, while the master Jichang Wang pleaded guilty in Gladstone's Magistrates Court and was fined $25,000.

Shenzhen Energy Transport Co said the damages sought were unrealistic.

It also said the reef was recovering naturally, which the Commonwealth disputed in court today.

More than 20 witnesses are expected to take the stand during the four-week hearing before Justice Andrew Greenwood.