Incidents of fishkill were reported in Mati City days after torrential rains were spawned by the low pressure area that has now become Tropical Depression Agaton, leading to flooding and excessive runoff from nearshore areas.
The fish die-off incidents happened off Purok Guang-guang along Pujada Bay, where fish cages are located.
About 20,000 fish reportedly died in the area.
Authorities from the Bureau of Fisheries and Aquatic Resources (BFAR) said the fishkill could be related to the weather condition affecting the city since last week.
BFAR 11 Director Fatma Idris said a huge volume of fresh water coming from land to the sea could have affected the salinity and the water temperature of Pujada Bay that killed the fish population, especially the juveniles.
Idris said government technicians have taken samples for analysis to determine the exact cause of the fishkill.
Local authorities, meanwhile, advised the people not to eat the fish as this could be harmful.
Mati City Mayor Carlo Rabat met with BFAR officials to discuss ways of helping the affected fishermen with their livelihood.