Three people were killed, one is missing and thousands fled their homes as a tropical storm battered the southern Philippines with strong winds and heavy rain, officials said Monday.

The storm, locally named "Seniang" and with winds of up to 80 kilometres (50 miles) per hour, slammed into the main southern island of Mindanao before dawn, then crossed to the central islands, the government weather station said.

In the Mindanao city of Tagum, a bus skidded off a rain-soaked road late Sunday, leaving one passenger dead and 17 injured, said provincial police chief Senior Superintendent Samuel Gadingan.

In the mountainous town of Monkayo, a 65-year-old man drowned as he tried to cross a river while one person was killed by a tree uprooted by fierce winds in Butuan City, other officials said.

Another man was swept away while collecting coconuts on a riverbank in Compostela town and is still missing, said regional disaster relief official Raul Villocino.

Landslides were also reported in the Monkayo area but no deaths were reported, Villocino added.

In Surigao del Sur province on Mindanao, a total of 13,740 people were evacuated in eight towns, Governor Johnny Pimentel told AFP.

"The rains are very strong and there has been no let-up in the last three days," Pimentel said.

Pimentel said he declared a "state of calamity" in the province to let local authorities tap into additional funding for relief supplies.

Flood waters as deep as five feet (1.5 metres) were reported in some areas as rescuers in rubber boats rushed to aid residents trapped in their homes, he said.

The number of evacuees may rise as rivers continue to swell, he said.

Winds had brought down trees and blown roofs off shanties, he said.

"This is the first time that my house was flooded," Agusan del Sur Vice Governor Santiago Cane said by phone.

Thousands of others were evacuated from lakeside and riverside communities in Agusan del Norte, said provincial disaster office staffer Erma Suyo.

Seniang was forecast to bring "heavy to intense" rains within its 300-kilometre diameter, as it packed wind gusts of 80 kilometres per hour.

The storm forced the cancellation of 32 domestic flights, the Manila airport authority said, while police said hundreds were stranded in seaports in the south.

The affected provinces are located in the Caraga region in northeast Mindanao, one of the Philippines' most flood-prone areas.

The country is battered by about 20 storms every year, many of them deadly.

Earlier this month Super Typhoon Hagupit left 18 people dead after it lashed central provinces with 210-kilometre per hour winds.

A year earlier, Super Typhoon Haiyan, the strongest ever to hit land, left 7,350 people dead or missing in the same region as it stirred up tsunami-like waves, wiping out entire towns.