The animal died after veterinarian Alex Collantes of the Davao Crocodile Park was called to check on its condition, GMA News reported.
The reason for Collantes visit and the cause of Lolong's death was not reported.
Bunawan Mayor Edwin Elorde said the animal had been acting irregularly since tropical cyclone Pablo devastated portions of Mindanao and Visayas in December.
Lolong was captured in 2011 after a years-long hunt for the animal thought to be responsible for a young girl's death in 2009 and the disappearance of fisherman, GMA reported.
The crocodile was 21-feet long and weighed more than one ton.
Officials with the Protected Areas and Wildlife Bureau will perform a necropsy on Lolong to determine a cause of death.
The mayor said he has asked the National Museum for help preserving the animal's remains.