The storm, locally named "Auring", hit Siargao island -- just off the main southern island of Mindanao -- with maximum gusts of 70 kilometres per hour.
The storm is forecast to move westward across the southern and central islands before exiting the archipelago by Tuesday, the government weather station said.
Floods have already occurred in some communities as rain had been falling even before the storm hit, said Amado Posas, the civil defence director of operations in the affected area.
He said disaster monitoring agencies had ordered pre-emptive evacuations even before the storm hit so there would be no casualties.
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The government has also suspended sea travel in affected areas.
The Philippine islands are often the first major land mass to be hit by storms that generate over the Pacific Ocean. It endures about 20 major storms each year, many of them deadly.
At least six people were killed and 18 others were missing after Typhoon Nock-Ten lashed the Philippines over the Christmas holidays.