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.
Tubod police officer Gerry Parami told the AFP news agency that there had been at least 19 deaths in the town, which is in Lanao del Norte.
"The river rose and most of the homes were swept away. The village is no longer there," he said.
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He said volunteers were digging through mud to try to recover bodies in the village of Dalama.
Another official told AFP that at least 10 people had died in the town of Piagapo, 10km east of Tubod.
"We've sent rescuers but they're making little progress due to the rocks," Saripada Pacasum said.
More deaths were reported in the towns of Sibuco and Salug.
Power cuts and the loss of communication lines have hampered rescue efforts.
After Storm Tembin skirts the southern edge of Palawan it is forecast to travel west, south of the Spratly Islands, reaching southern Vietnam in about three days
A week ago, Tropical Storm Kai-Tak hit the central Philippines, killing dozens.
The region is still recovering from Typhoon Haiyan, which killed more than 5,000 people and affected millions in 2013.
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