A 24-hour rescue effort near the northern town of Tuba failed to save the miner, who was trapped when rainwater brought by the cyclone seeped into the the small gold mine, said provincial police chief Benjamin Lusad.
Two of his colleagues were pulled from the shaft alive late Friday, Senior Superintendent Lusad told reporters.
Two men also drowned in the Bicol region southeast of Manila, the National Disaster Risk Reduction and Management Council said in its latest updated report.
While it avoided the Philippine land mass, Songda brought widespread floods and several landslides across the country, forcing more than 313,000 people to temporarily flee their homes, it added.
Songda was headed north for southern Japan on Saturday with peak winds of 140 kilometres (87 miles) an hour, the state weather service said.
An average of 20 storms and typhoons, some of them deadly, hit the Philippines every year. Tropical storm Aere left 31 people dead after cutting across Luzon island earlier in May.
(Uu.G003/H-AK)
Editor: Priyambodo RH
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