Reports Tuesday said police suspect the killings resulted from a domestic dispute.
The 7-year-old granddaughter of the farmhouse's owner, Yasuo Iihoshi, his wife Mihoko and an acquaintance, Fumiaki Matsuoka, were among those killed, Kyodo News Service reported, citing police.
The body of the man found near the bridge was thought to be Iihoshi's son, it said, AP reported.
Miyazaki prefectural police said officers found the bodies after a relative of the family contacted them, saying his calls had gone unanswered. They said some of the bodies had knife cuts.
Police said the seventh body, found in the river below the bridge, was of an unidentified man who apparently fled in the family's car.
The murder in the quiet hamlet raised alarm and town officials were urging residents to use caution and pick up their children after school instead of letting them walk home.
The town is near Takachiho valley, a popular tourist destination in southern Japan known for its scenic rice terraces.