According to the Philippine Weather Bureau, continuous intense rain will hover over the capital and neighbouring provinces.
Citizens were advised to watch for storm surges of up to 3 metres (10 feet) and flooding. Kammuri was expected to head out of the country on Thursday.
The Category 4 typhoon left a trail of fallen trees and overturned vehicles in its path. More than 200,000 people were evacuated.
Two people were killed; one man died after a tree fell on him.
“There are initial reports of houses blown away, power and communication lines down, roads blocked,” Red Cross chairman Dick Gordon said in an interview.
“If the typhoon hits a populous area like Manila, then it could bring flooding. But we can handle flooding,” he said.
Legazpi Airport in Albay was badly damaged with a portion of its roof blown off and windows broken.
Gordon said a clearer picture of the extent of the damage would emerge once roads were cleared of debris.
“Hopefully, we will get a free pass but it’s still too early to tell because many areas are still inaccessible,” he said.
Typhoon Kammuri, the 20th typhoon to hit the Philippines this year, rammed into the main Luzon island just before midnight local time, triggering mass evacuations in coastal areas and hillside communities.
The government’s disaster agency began moving people out of dozens of areas in southern Luzon on Monday as authorities raised the cyclone warning level for 35 provinces. People in the path of the typhoon were warned to be on alert for landslides, storm surges and floods amid strong winds and heavy rain.
Lovely Suarez, 48, was busy all morning knocking on her neighbours’ doors asking and sometimes begging them to evacuate.
Suarez lives in Baseco Manila in what has been classified as a danger zone as homes are surrounded by water on both sides.
“Most of the people follow. They started evacuating last night, starting with the children. But some are stubborn and won’t listen. They say they’re used to typhoons and have survived [and] they’ll survive this one,” said Suarez.
John Rey Cano, 29, a freelance researcher, braced himself for an evening of relentless rain. He stocked up on food and charged his mobile phone and power banks. He also made sure he had three days of spare clothes on hand.
A Manila resident all his life, Cano said he knows how torrential rain such as that from Typhoon Ketsana in 2009 can paralyse the city and cripple the services it depends on.
“We had no water, no electricity for days. I had to fetch water from a pump. I’m not taking my chances,” he told Al Jazeera.