The owners of a Chinese coal carrier that ran aground on the Great Barrier Reef will pay almost $40 million in an out-of-court settlement slammed by conservationists as late and inadequate.

Shenzhen Energy Transport Co Ltd and its insurer have for six years refused to accept responsibility for restitution relating to the 2010 accident.

Its 225-metre long, fully-laden Shen Neng 1 ran aground 100km east of Rockhampton at Douglas Shoal.

Environment Minister Josh Frydenberg on Monday announced a $39.3 million settlement had been reached.

“Our ongoing actions to pursue funds to clean up the pollution sends an unambiguous signal that damage to the Great Barrier Reef world heritage area is unacceptable,” he said.

The settlement included $35 million for the government to cover the cost of removing polluted rubble and $4.3 million for the Great Barrier Reef Marine Park Authority (GBRMPA).

Throughout the case, scientists were surveying the site and testing clean-up methods, GBRMPA chairman Dr Russell Reichelt said.

“Using this scientific and engineering work, the agency will use the funds from the settlement to initiate field operations to remove paint and rubble, enabling restoration of the natural ecological processes on this reef,” he said.

He described as “clearly unsatisfactory” the six-year delay.

“The Great Barrier Reef Marine Park is a place of outstanding beauty and diversity, and all who use it have a responsibility to ensure it remains this way for current and future generations,” Dr Reichelt said.

Greenpeace Australia spokeswoman Shani Tager said the amount was “woefully inadequate”, noting the government had previously pursued $120 million.

“It really shows that the coal industry and the Great Barrier Reef don’t mix and that we need to have stronger protections in place,” she said.

Some estimates placed the cost of the damage as high as $194 million – figures maritime insurer the London P&I Club dismissed as “unsubstantiated and unrealistic”.

Oil from Shen Neng 1 washed ashore at Northwest Island. Photo: AAP

The ship’s operator attempted to avoid a payout by arguing the reef was self-healing.

Australian Marine Conservation Society spokeswoman Shannon Hurley said experts had estimated the reef could take up to 20 years to recover from the incident.

“Clearly Australia can’t afford the damage that one ship, the Shen Neng 1, caused to the reef,” she said.

The London P&I Club expressed regret over the grounding and said it always wanted to reach a “fair and justifiable” settlement.

“The parties agree that the money to be paid is sufficient and appropriate under Australian and international maritime insurance agreements to cover required environmental remediation,” a spokesman said in a statement.

Much of the area had recovered naturally since 2010, the insurer added.

The anti-fouling paint spilled at the site contained a highly toxic component known as TBT, and copper and zinc, which could impact marine life on the sea floor for many decades if it remains there.

TBT has been banned since the spill.

The government estimated the clean-up operation would begin in mid-2017, however the depth of Douglas Shoal means work can only take place safely at certain times of the year.

-AAP