Local authorities said Trami dumped two months of rain, impacting over 6.7 million people across 17 of the country's regions, reports Xinhua news agency.
The search continues for 39 missing people who were either buried in landslides or washed away by the floods.
Trami, the 11th typhoon to hit the Philippines this year, barreled across the Philippines, leaving a trail of destruction with disastrous flooding and landslides on Luzon Island, particularly in the Bicol and Calabarzon regions, and areas in the central and southern Philippines.
Floodwaters crumbled highways and bridges, paralysing transport, and flooded homes with mud.
Three days after Trami exited the Philippines on Friday, disaster victims are still desperately waiting for food and clean water. Many areas still lack potable water or electricity.
Some victims forced to leave their flooded houses at the height of the flooding started returning to their homes as the flood receded on Saturday.
However, the NDRRMC said about 1 million displaced people were still in evacuation centres or staying with relatives.
Trami's estimated damage to infrastructure was 1.54 billion pesos (roughly US$26.35 million), while damage to agriculture was 2.5 billion pesos ($43 million).
The Philippines is bracing for more rains due to the impact of another tropical cyclone, Kong-rey, which intensified into a severe tropical storm Monday morning over the Philippine Sea, 755 km east of Luzon Island.
Kong-rey is the 12th tropical cyclone to hit the Philippines this year.
Moving westward at 20 km per hour, Kong-rey packs 95 km per hour winds and gusts of up to 115 km per hour.
"This tropical cyclone may also undergo rapid intensification," the bureau warned.
An average of 20 typhoons lash the Philippines yearly.