The coast guard first noticed an empty rowing boat rocking in the Rio Tuba river in the western island of Palawan late Thursday, said Lieutenant Greanata Jude.
When they approached, they found the fisherman's body tied to the vessel and in the mouth of the 12-to-15 feet crocodile who was trying to wrest the body away, Jude said.
"On the side of the boat was the body of the victim being bitten by a crocodile. The body was tied to the boat," she told AFP.
They recovered the body but it was not clear if the crocodile was hurt, she added.
Also Read
The fisherman was from a nearby village and had gone diving for sea cucumbers. He had tied the line to his boat to keep it from drifting away while he was underwater, coast guard official Jude said.
The boat apparently drifted from the sea into the Rio Tuba river although it is not clear where the fisherman encountered the crocodile, she added.
The river, about 730 kilometres west of Manila, is known to be inhabited by deadly saltwater crocodiles which sometimes attack humans.
The saltwater crocodile is found throughout Asia but the western island of Palawan, often called the Philippines' last frontier for its many forested areas, is one of the few areas where the animal is still common after suffering from hunting and habitat loss elsewhere.