Typhoon Kalmaegi is on a collision course with Leyte island, bringing 120-kilometre (75-mile) per hour winds and gusts of up to 150 kph, according to the national weather service.
"Evacuations are ongoing in Palo and Tanauan," said Leyte disaster official Roel Montesa, naming two of the towns hardest hit by storm surges in 2013, when Super Typhoon Haiyan killed more than 6,000 people.
Thousands of residents have also been evacuated since Sunday on neighbouring Samar island, where three-metre (10-foot) surges are predicted, according to civil defence official Randy Nicart.
"Some local governments are resorting to forced evacuations, including Guiuan town, where the storm is likely to make landfall," he said.
The Philippines is hit by an average of 20 storms and typhoons each year, routinely striking disaster-prone areas where millions live in poverty.
With Kalmaegi, the archipelago country has already reached that average, state weather service specialist Charmaine Varilla told AFP, adding that at least "three to five more" storms could be expected by December's end.
Just south of Leyte, in Dinagat Islands province, governor Nilo Demerey said 10,000 to 15,000 people had been pre-emptively moved to safer areas.
"We have been implementing preemptive evacuations for the past two days, while there is time," he told AFP.
Disaster official Joy Conales said residents of Dinagat's Loreto town were told to evacuate to higher ground.
The town has a one-storey-tall "wave breaker" dike intended to protect its centre from big waves.
Scientists warn that storms are becoming more powerful due to human-driven climate change.
Varilla said Tuesday that higher numbers of cyclones typically accompany La Nina, a naturally occurring climate pattern that cools surface temperatures in the central and eastern equatorial Pacific Ocean.
The Philippines was hit by two major storms in September, including Super Typhoon Ragasa, which toppled trees and tore the roofs off buildings, and killed 14 people in neighbouring Taiwan.
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