The storm has affected over 1.8 million people and 63 people remain missing, NDRRMC said in its Monday report.
On Saturday, NDRRMC said that the death toll from Nalgae was up to 72, while 33 people were injured.
According to the Monday update from the risk reduction council, the death toll has gone up to 98, while a total of 69 people were reported injured.
Nalgae has forced over 12,100 people to evacuate and many remain in the 113 temporary shelters that have been set up across the country.
Nearly 3,500 houses have been damaged by the storm, while 689 homes have been destroyed.
More than 70 roads, 16 bridges and 58 sea ports have been damaged. Power disruptions have been reported across the country.