The Great Barrier Reef Marine Park Authority (GBRMPA) says it cannot afford to clean up all the toxic mess left over from the grounding of a bulk coal carrier on the reef in 2010.

Chinese ship Shen Neng One ran aground on Douglas Shoal off the central Queensland coast on April 3, 2010, after veering more than 10 kilometres outside the shipping lane.

The grounding damaged one of the ship's fuel tanks, resulting in a four-kilometre-long slick of heavy fuel oil and leaving toxic antifouling paint embedded in the sea floor.

It also carved a three-kilometre-long, 400,000-square-metre scar in and around Douglas Shoal, about 120 kilometres east of Rockhanmpton, which was the largest known damage to the Great Barrier Reef caused by a ship.

The Federal Government is pursuing legal action against the owner, Shenzhen Energy Company.

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GBRMPA chief executive officer Russell Reichelt said the clean-up needed to happen "urgently".

"It's our view and was briefed to the Minister — the Minister's view — [this] should be done as soon as we possibly can," Dr Reichelt told Senate Estimates.

"It's preventing the natural recovery process in the more than 50 hectares of sea floor."

Dr Reichelt said GBRMPA did not have the budget to do the clean-up itself, so legal action was required.

"[It's about] resourcing," he said.

"It would be a substantial cost beyond the capacity of our budget ... it would exceed $50 million.

"It remains our best avenue to achieve those funds.

"It is an issue for the authority and we've repeatedly made it clear through the courts to the company."

Shen Neng One caused unprecedented damage and in 2012, the captain of the ship was fined $25,000 and the second-in-charge was sentenced to three months' jail.