Twelve Chinese fishermen were handed long prison terms on Tuesday for illegal fishing in the Philippines after their ship ran aground on a World Heritage-listed coral reef, a court official said.

The 12 were arrested at the Tubbataha Reef, a marine sanctuary in the western Philippines famed as a pristine dive spot, in April last year after their 48-metre (157-foot) boat hit and badly damaged it.

Boat captain Liu Chiangjie and his crew had pleaded not guilty, telling the court in the western city of Puerto Princesa that they had merely got lost but regional trial court judge Ambrosio de Luna rejected the explanation as "highly incredible and unbelievable".

The court imposed the maximum punishment of 12 years for the boat captain and prison terms of between six and 10 years for the rest of the crew, clerk of court Hazel Alaska told AFP.

The 12 told the court they would appeal against the ruling.

All were found guilty of violating the anti-poaching provisions of a 2009 law that gave the Tubbataha Reef protected status, according to Alaska.

The fishermen were also fined $100,000 each, while their boat was forfeited, Alaska added.

They were the first foreigners to be found guilty of violating the law, according to Herminia Caabay, legal officer for a council that helps the western province of Palawan protect its natural resources.

- Dead pangolins in boat -

The fishermen were still on trial for possession of protected species within the park, Alaska said, a crime punishable by up to 20 years in prison.

The Philippine coast guard had said hundreds of dead and frozen pangolins were seized from the Chinese fishing boat.

Pangolins are widely hunted in parts of Asia, including Palawan, for their meat, skin and scales.

In China they are considered a delicacy and to have medicinal qualities.

The boat captain had earlier testified during the trial that the boat's global positioning system navigational equipment had broken down on their way home from Indonesia, and as a result they did not know where they were.

The 12 are among dozens of Chinese and Vietnamese fishermen who are detained in Palawan for illegal fishing.

Among the others are nine Chinese fishermen who were arrested on May 6 off Half Moon Shoal, a South China Sea outcrop claimed by both China and the Philippines.

However the 97,000-hectare (230,000-acre) Tubbataha Reef, which was listed as a World Heritage Site by the United Nations in 1993, is in a part of the Sulu Sea claimed only by the Philippines.

It requires long sailing in Philippine waters to reach.

Asked if the decision would affect ties with China, Foreign Department spokesman Charles Jose said in a statement: "The verdict was based on applicable Philippine laws. And the place where these Chinese fishermen were apprehended in April 2013 is part of the Philippines' internal waters where it has exclusive sovereignty."

The Chinese boat ran aground less than three months after a US minesweeper ploughed into the reef while transiting through the area. The US Navy had to cut up the vessel in a salvage operation that took 10 weeks.

The Philippines fined the United States 58 million pesos ($1.33 million) for damaging the reef, but laid no criminal charges.

"This is a breakthrough in our campaign against environmental degradation," chief provincial prosecutor Alen Rodriguez told AFP after the court handed down its verdicts.

"I hope this will be the start of a winning streak."