Environmental officer Job Tagle said he found about a dozen people with knives running away with big basins of meat carved from the whale shark when he reached the village of Bio-os in the central Philippines on Tuesday.

Tagle said only the head of the whale shark - the world's biggest fish species - was left when he and police arrived.

It took at least 10 men to carry the head, which weighed about 200kg, onto a van. It had what looked like several bullet and spear wounds and was later buried, he said.

The owner of the fish pen, located about 500 metres from shore, said the animal was dead when he found it, but police suspect it was killed based on its wounds, Tagle added.

An official of the Department of Environment and Natural Resources in Negros Oriental province, Oscar Moncopa, said charges will be filed against the owner.

Conservation group WWF-Philippines said possession or slaughter of a whale shark can be punished by up to four years' imprisonment plus a fine of up to 10,000 pesos ($A237).

In February, another 5-1/2-metre whale shark was found dead and the Bureau of Fisheries and WWF offered a $US2,170 ($A2,239) reward for information about the culprits. No one has been arrested.

Whale sharks have been hunted for decades and 2.2 pounds (a kilogram) of dried fins can fetch up to $US800 ($A825) on the black market.