His father Takayuki Tanooka, 44, had initially told police that he, his wife and daughter had become separated from Yamato while foraging for edible plants.
However, hours later he confessed that he had in fact made Yamato get out of the family car and left him briefly by the roadside in an attempt to discipline him after he was throwing stones at people earlier in the day.
A soldier eventually found Yamato found by chance last Friday in an empty military hut more than 4.8km from where he was left and he was airlifted to hospital where he has been treated for mild dehydration and mild scratches.
Tanooka, who has regretfully admitted his actions were excessive, has described how he apologised to his son in hospital.
"I said to him, 'Dad made you go though such a hard time. I am sorry'," Tanooka told the broadcaster TBS.
He tearfully added: "And then, my son said, 'You are a good dad. I forgive you'."
The boy revealed harrowing details of his ordeal to police when they interviewed him yesterday, according to media reports.
After tearfully chasing his parent's car, the boy was afraid of staying in the forest and reportedly walked for about five hours in the dark along a path until he came to the hut.
As the days passed, the child reportedly spent time walking around the drill field near the single storey hut when the sun shone but did not wander far.
He also heard the sound of helicopters and cries of wild animals but did not encounter any people, although he knew his family would be looking for him, local reports stated.
The schoolboy has dropped from his initial weight of 21kg to less than 19kg, although he is believed to be recovering quickly in hospital, finishing each meal.
Yamato, who has been passing time with his family by drawing in a notepad and playing cards, is expected to be discharged from hospital today.