Three bodies were found after the two-story home of a doctor in Tawaramoto, Nara Prefecture, burned down early Tuesday, police said.
Four of the five members of the doctor's family living in the home are listed as missing, police said.
The doctor, Motoyoshi Yoshikawa, 47, was working overnight at a hospital in neighboring Mie Prefecture.
The four missing are his wife, Minka, 38, who is also a doctor, along with their 16-year-old son, Yuta, 7-year-old son, Yoshiki, and 5-year-old daughter, Yumin.
Police believe the three bodies are those of the wife and two of the three children and were trying to locate the fourth member of the family. The cause of the fire was not yet known.