The landslide hit the mountainous village of Masara in Davao de Oro province on Tuesday evening after weeks of heavy rain.
The Davao de Oro regional government said in a Facebook post that 54 bodies had been recovered.
She added that at least 32 residents survived injuries, but 63 were still missing.
Among the missing are miners who were waiting on two buses to return to their homes when the landslide occurred and buried them.
The search operation was hampered by bad weather conditions and fears of more landslides.
Disaster response officials said that more than 1,100 families had been moved to evacuation centers for their safety.
The area had been subjected to heavy rains in the weeks before the landslide.
Officials said the earthquakes also destroyed homes and buildings in the area in recent months.
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