Storm Tembin brought flash flooding and mudslides to parts of Mindanao island.
Two towns badly hit were Tubod and Piagapo, where a number of homes were buried by boulders.
Tembin, with winds of up to 80km/h (50 mph), has now passed across Mindanao and is heading towards the southern tip of Palawan before moving further west.
The Philippines suffers regularly from deadly tropical storms, although Mindanao is not often hit.
Tembin, known as Vinta in the Philippines, started lashing Mindanao on Friday, with a state of emergency declared in some parts, including the Lanao del Norte and Lanao del Sur regions.
The region is still recovering from Typhoon Haiyan, which killed more than 5,000 people and affected millions in 2013.