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Police found the remains in a house owned by 72-year-old Yasuo Iihoshi, after one of her family reported that her calls were unanswered, according to the Miyazaki Prefect's police.
One of the bodies, a woman, was discovered outside the property, while three men and two other women were found inside the house.
Japan, one of the safest countries in the world, has a very low murder rate and mass killings are rare. Due to Japan's strict firearms laws, knives are more commonly used in infrequent attacks.
During killings in Takachiho, at least some of the victims were stabbed, local media reported. The weapon of crime has not been found.
Authorities released the names of the victims, including Yasuo Iihoshi, his wife Mihoko, 66, their granddaughter Yui, 7, his daughter-in-law Mikiko, 41, and his elderly grandson 21 years old. Takumi.
They are all members of the immediate family of Iihoshi's second son, Masahiro.
The sixth victim, 44-year-old Fumiaki Matsuoka, is not related to the family, but is a friend of Masahiro's.
Masahiro Iihoshi has disappeared since the discovery of the bodies. The police also discovered a seventh body under a bridge across the Gokase River.
Famous tourist destination
Kyushu City is famous for the nearby Takachiho Scenic Gorge, and is an important site for Shinto myth and legend.
The most deadly mass murders perpetrated by Japan since the Second World War were recorded in 2016. At least 19 people were killed and 26 wounded during a stabbing attack in an establishment for disabled people west of Tokyo.
Satoshi Uematsu, the suspect in the case, had written a letter several months before the incident, in which he claimed that he had "the ability to kill 470 disabled people".
The death toll from the attack eclipsed the infamous Aum Shinrikyo sarin gas attack in 1995, which killed 13 people and wounded more than 6,000 others.
