Civil defense officials have been put on “red alert”, as Nock-Ten is due to hit Manila on December 26.
The typhoon has weakened since making landfall on the eastern coast on December 25, but it still packs winds up to 87mph, meteorologists say.
Three people were reported killed in Albay province, south-east of Manila.
Nock-Ten (known as Nina in the Philippines) has cut power lines and uprooted trees.
Manila’s civil defense office warned that the capital could be hit by “heavy to intense rains, flash floods and severe winds”.
The coastguard has ordered beaches south of Manila to be cleared.
The storm hit the coast near Catanduanes Island on Christmas Day, knocking out power.
Hours later, local media reported that in Albay province a couple were swept away in a flash flood and an elderly man was killed by a collapsing wall.
About 100,000 people had been earlier moved from areas at risk in the Bicol region amid fears of widespread flooding and possible landslides.
There were fears Filipinos would ignore evacuation warnings to stay at home with family at Christmas, the biggest holiday in the largely Catholic nation.
Dozens of ports remain closed, with warnings of high waves.
Nock-Ten is expected to pass across the main island of Luzon, before heading into the South China Sea.
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