The victims included a 23-year-old mother and her two children, aged 2 and 6 years, whose house was buried in a landslide in the town of Carrascal in Surigao del Sur province, 786 kilometres south of Manila.
A 10-year-old was also killed in a separate landslide in the same town, according to local disaster relief officials.
More than 1,800 residents were forced to flee their homes in Surigao del Sur and the nearby province of Surigao del Norte due to tropical storm Sanba, which made landfall Tuesday morning, the national disaster relief agency said.
The tropical depression was packing maximum winds of 55 kilometres per hour (kph) and gusts of up to 75 kph as it moved west-northwest at 25 kph, it added. It was expected to be out of the country by Friday morning.
An average of 20 typhoons batter the Philippines every year.