Colonel Ernesto Torres, spokesman for the National Disaster Co-ordinating Council (NDCC), said people living in coastal areas, near river banks, mountain slopes "and other landslide-prone areas should evacuate now".
Since Friday, Torres said, government agencies had been "prepositioning relief goods" in the sparsely populated Batan island group near Taiwan, the northern city of Tuguegarao and key population centres in the Cordillera range, which were hard hit by landslides during the previous tropical storms.
The weather service warned that seven dams in northern Luzon had been releasing water in anticipation of heavy rains brought by Typhoon Lupit.
Widespread flooding had killed 380 people and displaced 4.34 million others in and around Manila on September 26 as Tropical Storm Ketsana brought record rainfall to the region, the NDCC said in an updated toll.
Tropical Storm Parma hit northern Luzon a week later and hovered over the region for a week, triggering landslides and floods that left 438 people dead and displaced 3.8 million others, it added.
About 266,000 people remain in crowded evacuation camps more than two weeks later, and a bacteria-borne disease called leptospirosis has killed another 89 people in flooded areas since then, the health department said.