The male crocodile had to be tied, blindfolded and carried by more than 10 men. It was estimated to weigh up to 770 pounds (350 kilos).
The croc was captured in a trap set up along the Rio Tuba river to hunt for the crocodile that ate the fisherman's legs, said Alex Marcaida, a spokesman for an environment council in Palawan province.
The crocodile was caught near where the man's partial remains were found in Bataraza township of western Palawan province.
It will be induced to vomit to see if its stomach contains human tissues, though Marcaida said it might be too late to know for sure whether the croc killed the man. An 8-foot (2.4 meter) crocodile captured earlier had no trace of human tissues in its stomach.
Crocodylus porosus is the world's largest living reptile species, and full-grown males can reach the length of the one captured.
The species thrives in mangrove areas, and over the last 10 years, crocodiles have killed at least three people in Palawan, Marcaida said.
Wildlife workers only catch "problem crocodiles" but generally leave crocodiles in their natural habitat. Those caught are brought to a crocodile farm and wildlife center in the provincial capital, Puerto Princesa.
The killings may have occurred, he said, because the crocodiles' natural habitat have been disturbed. Some residents near where the crocodile was caught Monday have built closer to the mangrove areas, even putting up backyard piggeries that jut out onto the river, Marcaida added.
Crocodiles usually go back to where they had their last meal, he said, making it necessary to remove the crocodile.