Two of the victims drowned in flash floods while the other was electrocuted due to inundation.
The minimal tropical storm, which made landfall well before dawn on Saturday, took just over a day to pass over the provinces of Cebu and Southern Leyte before dissipating over the South China Sea.
Kajiki also came in the wake of a tropical depression locally dubbed Agaton, which left more than 70 people dead from floods and landslides in the same region just a week earlier.
Nearly 18,000 were displaced by the back-to-back cyclones that affected 25 provinces in total, according to the national disaster relief agency.
Tropical Storm Kajiki Track
Satellite Loop Data: CIMSS