Australian Federal Police have arrested the captain of a Chinese coal ship sailing through part of the Great Barrier Reef Marine Park.

Reports say the captain has been charged for being the master of a ship without a pilot, and could end up with a maximum $85,000 fine.

A Newcastle court will this week hear allegations that a bulk carrier - the China Steel Developer - left Mackay on January 1 and sailed through a deep water channel near Creal Reef without a pilot.

It is believed that the ship took a load of coal to China before returning to Australia.

When it anchored off Newcastle last week, AFP officers moved in to arrest Captain Lu.

The most recent related event came in 2010, when a Chinese bulk carrier ran aground on a reef off central Queensland, and dumped a four-kilometre-long slick of heavy fuel oil from its ruptured tanks,.

It also cut a 400,000-square-metre gash into the Great Barrier Reef.

Experts say the coral is not growing back properly because of toxic anti-fouling paint used on the hull of the Chinese ship, the Shen Neng 1.

The Shen Neng 1’s first mate served three months in prison and the vessel’s master was fined $25,000.

About 4,500 ships travel through the Great Barrier Reef to Queensland ports every year, and conservationists say with resource exports increasing all the time, such events are only doomed to be repeated.