The BBC's Kate McGeown in Manila says many residents are still on rooftops awaiting rescue from the first storm.
The Philippines suffers frequent typhoons, about 20 a year.
Nalgae made landfall in the eastern province of Isabela on Saturday with winds of up to 160km/h (100mph) and is heading west across the main island of Luzon.
First reports speak of material damage across the affected region, but there has been no word so far of casualties.
The storm is taking much the same route as Typhoon Nesat which hit the country on Tuesday leaving at least 50 people dead and thousands homeless.
Tens of thousands of residents have moved into evacuation centres or the homes of relatives or friends, but many areas are still heavily flooded from the earlier storm.
Officials say more than a million of Luzon's 48 million inhabitants remain trapped by the floods.
Several towns remain submerged.
Provincial disaster official Raul Agustin told ABS-CBN television that marooned flood victims were often reluctant to leave for fear their homes would be looted.
"When we send out rescue teams to help them, they ask for food instead," he said.