The death toll from a tropical storm in the southern Philippines climbed swiftly to 133 on Saturday, as rescuers pulled dozens of bodies from a swollen river, police said.

Tropical Storm Tembin has lashed the nation's second largest island of Mindanao since Friday, triggering flash floods and mudslides.

Rescuers retrieved 36 bodies from the Salog river in Mindanao on Saturday, as officials reported more fatalities in the impoverished Zamboanga peninsula.

It was forecast to smash into the tip of the western island of Palawan late Saturday, the state weather service said.

“The river rose and most of the homes were swept away. The village is no longer there,” Tubod police officer Gerry Parami told AFP by telephone.

Police, soldiers and volunteers used shovels to dig through mud and debris in a bid to recover bodies in Dalama, a farming village of about 2,000 people near Tubod, Parami added.

Boulders brought down by flash floods also buried around 40 houses in the town of Piagapo, killing at least 10 people, civil defence officer Saripada Pacasum told AFP.

“We've sent rescuers but they're making little progress due to the rocks,” he said.

The Philippines is pummelled by 20 major storms each year on average, many of them deadly. But Mindanao, home to 20 million people, is rarely hit by these cyclones.

Eight other people were killed by floods elsewhere on Lanao del Sur province, Pacasum said.

Police said three people each died from landslides in the provinces of Bukidnon and Zamboanga Sibugay, while one fatality was also reported in Iligan city.

Four people were listed as missing after being buried in landslides or being swept away by floodwaters, while more than 12,000 have fled their homes, they added.

After slicing across Mindanao on Friday, Tembin sped west over the Sulu Sea with gusts of 95 kilometres an hour.

Tembin struck less than a week after Tropical Storm Kai-Tak devastated the central Philippines, leaving 54 dead and 24 missing.

The deadliest typhoon to hit the country was Haiyan, which left 7,350 people dead and destroyed entire towns in heavily populated areas of the central Philippines in November 2013.