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The eye of Typhoon Rammasun, the strongest storm to hit the country this year, passed to the south of Manila after cutting a path through eastern islands, toppling trees and power lines and causing electrocutions and blackouts.
It brought storm surges to Manila Bay and prompted disaster officials to evacuate slum-dwellers on the capital's outskirts.
Richard Gordon, chairman of the Philippine National Red Cross, said there was minimal damage in the capital but staff were trying to rescue people trapped by fallen debris in Batangas City to the south where two people were electrocuted.
"We have not received reports of major flooding in Metro Manila because the typhoon did not bring rain, but the winds were strong," he said.
Parts of the Philippines are still recovering from Typhoon Haiyan, one of the biggest cyclones known to have made landfall anywhere. It killed more than 6100 people last November in the central provinces, many in tsunami-like sea surges, and left millions homeless.
Rhea Catada, who works for Oxfam in Tacloban, which suffered the brunt of Haiyan, said thousands of people in tents and coastal villages had been evacuated to higher ground since Monday.
"They are scared because their experiences during Haiyan last year are still fresh," she said. "Now they are evacuating voluntarily and leaving behind their belongings."
Tropical Storm Risk, which monitors cyclones, labelled Rammasun a category-two storm on a scale of one to five as it headed west into the South China Sea. Super typhoon Haiyan was category five.
A 25-year-old woman was killed when she was hit by a falling electricity pole as Rammasun hit the east coast on Tuesday, the Philippine disaster agency said. A pregnant woman was killed when a house wall collapsed in Lucena City in Quezon province south of the capital.
Nearly 150,000 people have been evacuated from their homes in low-lying and coastal areas. More than 60 international and domestic flights have been cancelled over the past two days.
Trading at the Philippine Stock Exchange and Philippine Dealing System, used for foreign exchange trading, were suspended after government offices were ordered shut.