The chief officer of a Japanese-owned ship was fined $32,500 in the Gladstone Magistrates Court today for entering a restricted area in the Great Barrier Reef Marine Park.

He was in charge of the ship U-SEA Panache when it transited the area between One Tree Island and Lamont Reef in the Capricorn Bunker Group at about 04.30am on Wednesday 9 March 2011.

The Great Barrier Reef Marine Park Act 1975 prohibits ships from entering some areas in the Marine Park including the cluster of islands that make up the Capricorn-Bunker Group.

The maximum penalty for crew for this type of offence is $110,000.

Great Barrier Reef Marine Park Authority Chairman Russell Reichelt said the majority of shipping activities were carried out within the rules.

"The Great Barrier Reef Marine Park is a multiple use area and commercial and recreational activities are allowed, but they must be carried out legally," he said.

"Shipping is restricted in some areas due to the risk of grounding or causing damage to the environment.

"These restricted locations typically contain coral reefs and sensitive habitats, and these can present navigation hazards.

"The Capricorn Bunker Group particularly presents a high level of risk to large ships."

The Capricorn-Bunker Group is special and unique and was the first part of the Great Barrier Reef Marine Park to be declared and protected. It is also a popular tourist site.

The ship was tracked by two electronic vessel tracking systems managed by the Australian Maritime Safety Authority.

On Thursday 10 March inspectors from the Great Barrier Reef Marine Park Authority, Queensland Water Police and Australian Maritime Safety Authority boarded the ship when it docked in Gladstone.

There are 10 major trading ports along the Great Barrier Reef coast and the latest statistics show that over 3500 ships operate in the Great Barrier Reef, making over 9700 voyages each year.

Most routine shipping activities have negligible consequences on the Marine Park. Almost all ships travel safely along the designated shipping routes of the Great Barrier Reef with little, if any, impact.