Nine people died in Mountain Province and Benguet in the northern highlands after their houses were buried in rocks and mud. A man was killed in nearby Ilocos Norte province after he was hit by a falling tree, the national disaster council said in a report.
Three people were reported missing in flooded areas while seven others were injured. Close to 13,000 people had been evacuated by nightfall, the report said.
Typhoon Goni was 130 kilometres northeast of the Batanes island chain this evening, with winds of up to 185kph, according to the state weather bureau.
"The Abra river has turned into an ocean," Bersamin told DZMM radio.
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"The rains were much stronger than we expected," he said.
Thirteen domestic flights were cancelled today, the disaster council said.
The storm is the ninth out of an average of 20 that hit the Philippines each year and is now heading to Taiwan, the weather bureau said.
Taiwan has evacuated people from outlying islands and troops are on standby for disaster relief as it takes precautions against heavy rains expected this weekend.
While the chance of Goni making landfall in Taiwan has diminished, the typhoon will bring heavy rains to most of the island today and tomorrow, with mountainous areas in eastern Hualien and Yilan counties expected to see torrential downpours.
Areas at risk included the hot spring town of Wulai that was devastated by Typhoon Soudelor just two weeks ago. The popular tourist destination is still struggling to repair roads damaged by mudslides and the town remains cut off from regular water and power supplies.
At least 1,700 tourists have already been evacuated from Taiwan's outlying Green and Orchid islands. Offices and schools have been closed there since yesterday. Some ferry services and domestic flights have been cancelled, but international flights have yet to be affected.