THE death toll from a tropical storm in the southern Philippines has climbed swiftly nearly 200 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, reports news.com.au.

At least 160 people are still unaccounted for.

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

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Romina Marasigan of the government's disaster-response agency said landslides and flash floods triggered by Tropical Storm Tembin inflicted most of the deaths in the hard-hit provinces of Lanao del Norte and Lanao del Sur and on the Zamboanga Peninsula.

Officials were getting more details to validate the reported casualties, Ms Marasigan said.

It's the latest disaster to hit the Philippines, which is battered by about 20 typhoons and storms each year, making the archipelago that lies on the Pacific typhoon belt one of the world's most disaster-prone countries.

Mayor Bong Edding of Zamboanga del Norte province's Sibuco town said by phone that a search and rescue operation was underway for more than 30 people swept away by flash floods in the fishing village of Anungan. Five bodies have been recovered so far in the village.

"The floodwaters from the mountain came down so fast and swept away people and houses," Mr Edding said. "It's really sad because Christmas is just a few days away, but these things happen beyond our control."

Mr Edding blamed years of logging in the mountains near Anungan for the tragedy that unfolded on Friday, adding that he and other officials would move to halt the logging operations.

The rest of the deaths were reported in Lanao del Norte, where floodwaters from a mountain also swept away several riverside houses and villagers, and Lanao del Sur, police and officials said.

Rescuers are racing against time to pull dozens of bodies from a swollen river after a tropical storm unleashed flash floods and set off landslides in the southern Philippines. Photo / AP
Rescuers are racing against time to pull dozens of bodies from a swollen river after a tropical storm unleashed flash floods and set off landslides in the southern Philippines. Photo / AP

Thousands of villagers moved to emergency shelters and thousands more were stranded in airports and seaports after the coast guard prohibited ferries from venturing out in the rough seas and several flights were cancelled.

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An inter-island ferry sank off northeastern Quezon province on Thursday after being lashed by fierce winds and big waves, leaving at least five dead. More than 250 passengers and crewmen were rescued.

Tembin, locally known as Vinta, was packing maximum sustained winds of 80 kilometres (50 miles) per hour and gusts of up to 95km/h, and is forecast to blow away from the southern Philippines on Sunday toward the South China Sea, moving closer to Vietnam.

"It is unfortunate that another tropical cyclone, Vinta, made its presence felt so near Christmas," presidential spokesman Harry Roque Jr. said, adding that food packs and other aid were being distributed in storm-hit communities.

Earlier in the week, a tropical storm left more than 50 people dead and 31 others missing, mostly due to landslides, and damaged more than 10,000 houses in the central Philippines before weakening and blowing into the South China Sea.

Among the areas battered by Tembin was Marawi, a lakeside city in Lanao del Sur that is still recovering from a five-month siege by pro-Islamic State group extremists that left more than 1000 people dead.