The 7.8-magnitude tremor in southern Mindanao island on June 8 also left at least 40 people missing, according to updated tolls from the disaster agency.
Local residents first reported the geological phenomenon known as "coastal uplift" two days after the quake, which extended the shoreline by as much as 200m in some places, the environment department said.
A shifting of the Cotabato Trench "pushed upward part of the coastlines of Sarangani and Davao Occidental (provinces)... exposing the bottom of the sea that was originally submerged", the Philippine Institute of Volcanology and Seismology said in a statement.
"Approximately 2 m was the mapped uplift."
The Cotabato Trench, which lies as close as 50 km off the coast of southern Mindanao, is the site of frequent seismic activity, including a "swarm" of thousands of mostly small earthquakes recorded in January.
