Typhoon Bopha made landfall on Mindanao early on Tuesday, bringing heavy rain and wind gusts of 210 km/h (130 mph).
At least four people died in the storm, which caused power cuts, travel disruption and flooding in areas at risk of landslides.
Bopha comes a year after Typhoon Washi killed more than 1,500 people in the southern Philippines.
On Monday, President Benigno Aquino urged people in the typhoon’s path to take Typhoon Bopha seriously.
“It could be the strongest to hit the country this year,” he said.
“But we can minimize the damage and loss of lives if we help each other.”
In the gold-mining province of Compostela Valley, the extreme weather forced a wall of mud to fall on to a house, killing some of those inside, the Associated Press reports.
Benito Ramos, of the national disaster agency, said the death toll was expected to rise once soldiers and police gained access to the far-flung villages isolated by floods, fallen trees and damaged communications.
According to one report, quoting a military spokesman, about 20 people including six soldiers were missing after fast-moving water swept through an army base.
The eye of the 600-km wide storm was moving west at 26 km/h and was expected to sweep over southern and central provinces before reaching the South China Sea on Thursday, forecasters said.
The Philippines is struck by several typhoons and tropical storms every year.
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