Civil defence officials have been put on "red alert", as the storm is due to hit the city later on Monday.
The storm has weakened since making landfall on the eastern coast on Sunday, but it still packs winds up to 140 km/h (87mph), meteorologists say.
The storm cut power lines and uprooted trees, but no deaths were reported.
Manila's civil defence office warned that the capital could be hit by "heavy to intense rains, flash floods and severe winds".
"Our local disaster councils are on red alert," Mina Marasigan, spokeswoman of the country's disaster monitoring council, was quoted as saying by the AFP news agency.
"We have pre-positioned relief supplies and rescue and (road) clearing equipment in Metro Manila," she added.
Nock-Ten (known as Nina in the Philippines) hit the coast near Catanduanes island on Sunday.Some 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.
The typhoon is expected to pass across the main island of Luzon, before heading into the South China Sea.
In October, Super Typhoon Haima hit the country, killing at least four people.
In 2013, super typhoon Haiyan claimed more than 7,350 lives.
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