At least 17 people are still missing and more than 40,000 were displaced nationwide due to the storm, the civil defence office said.
Usman brought heavy rains that caused floods and loosened the soil, triggering landslides in some areas.
Rescue teams were still searching for several missing in the affected areas, emergency officials said.
Typhoon Mangkhut, the strongest typhoon of 2018, battered the southeast Asian country in September, packing winds of up to 270 kph (165 mph) and wreaking devastation across the northern Philippines.
A disaster agency spokesperson said the people, including a three-year-old boy, were reported dead as of this morning after a tropical cyclone barrelled through the eastern Visayas and Bicol regions yesterday.
In Eastern Visayas, three people were reported killed in a landslide and three due to drowning.
More than 22,000 people fled their homes ahead of the storm, which destroyed rice and corn crops and left some roads and bridges inaccessible, according to regional disaster officials.
Thousands of passengers were stranded at seaports, airports and bus terminals as dozens of inter-island trips were cancelled.
The weather bureau said the tropical depression, locally named Usman, has weakened into a low-pressure area after making landfall but warned that eastern and central provinces would continue to experience rains.
A cold front and the northeast monsoon were also bringing bad weather over the capital, Manila, and other parts of the country, which could dampen usually rowdy New Year's Eve celebrations.
The worst storm to hit the Philippines in a generation occurred in 2013, when Super Typhoon Yolanda killed more than 6,000 people and displaced almost 4 million others.