A man went missing and thousands of people in the Philippines were sheltering in evacuation centres Monday as Tropical Storm Jelawat hit the large southern island of Mindanao, causing scattered flooding and power cuts.

The storm weakened as it raked across Mindanao after making landfall in the morning, but the state weather service said the threat of floods and landslides remained.

Police in Manay municipality, where Jelawat made landfall, reported one man missing at the swollen Casaoman River that bisects the coastal town of about 40,000 people.

"A local man ignored warnings and went to gather coconuts floating on the river. It is suspected he's been swept away," acting Manay police chief Major Meliton Sango said.

Two areas of Manay reported knee-deep floodwaters as the river overflowed, the officer told AFP by telephone.

The civil defence office in Manila reported two damaged houses in Cortes, another town on Mindanao's east coast, along with power cuts in three other towns.

A total of 11,729 residents had been evacuated from Mindanao's east and north coast ahead of landfall as a precaution.

They were advised by authorities to remain at emergency shelters for now.

Jelawat was forecast to plough across the south of the country for the rest of the day, with the weather service warning of heavy rain, especially in the mountainous interior.

"Under these conditions, flooding and rain-induced landslides are likely especially in areas that are highly or very highly susceptible to these hazards," its latest storm bulletin said.

The coast guard reported widespread shipping disruptions as sailing restrictions were put in place to prevent accidents in rough seas.

More than 100 vessels were stranded or sought shelter at ports, with more than 5,000 passengers stuck at the port of Manila as ferry services to the central and southern Philippines were suspended, it said.

About 20 storms and typhoons hit the country or its surrounding waters per year, killing hundreds and keeping many of the areas of the country poor.

Jelawat is only the 11th this year, so far equalling a record low set in 1998, according to weather service data.