Takayuki Tanooka, 44, and his wife briefly left Yamato Tanooka by the side of the road on the northern island of Hokkaido on 28 May as punishment.
When they came back he was gone. A huge search was launched and the boy was found at a military base on Friday.
Yamato was taken to hospital but was discharged on Tuesday.
The case sparked a debate in Japan about parenting.
Mr Tanooka told broadcaster TBS in an interview aired on Monday: "I said to him, 'Dad made you go though such a hard time. I am sorry'."
"And then, my son said, 'You are a good dad. I forgive you'."
The boy was found on Friday morning in a hut on a military drill field, some 5.5km (3.4 miles) from where he was left as a punishment for throwing stones at people and cars.
He said he had lost his sense of direction from crying and walked for about five hours before arriving at the building where he was found, according to The Mainichi newspaper.
He slept between two mattresses and "met no-one".
He said he drank water from a tap at the facility but ate nothing for six days, the newspaper said.
When found, Yamato was lightly dehydrated, malnourished and had scrapes on his arms and legs but was said to be otherwise in good health.
Police have said they will not be pressing charges against the parents, local media reported.
The father of a seven-year-old Japanese boy who was found alive after six nights alone in a dense forest says his son has forgiven him.