He was discovered in a small building at a military exercise ground about 2.5 miles (4 kilometers) from the spot where he was left alone at the roadside for a short time by his parents for being naughty.
Takayuki Tanooka, the father of the boy, said he was "very sorry" for what happened to his son and regretted the punishment.
"I told my son that I am sorry that I made him go through a very hard situation. He nodded to me," Tanooka told CNN affiliate TV Asahi Friday after being reunited with his son.
"I have been raising him with lots of love," he said. "I would like to pour a lot more love over him from now on, and watch him growing up."
"I never thought the situation would develop in such a way. I thought it would be good for him, but it was too much," he added.
Hungry but uninjured
Japan's Self-Defense Forces personnel found Yamato Tanooka on the premises of the military's Kamagatame exercise field Friday morning, said Satoshi Saito, a spokesperson for the local fire department.
An SDF member who found the boy said he was hungry. The member gave him water and a rice ball. The member said the boy was fine and talking normally.
The boy told police he reached the building the first night he was missing, local media said.
He appeared to be in good condition for someone who had spent seven days without food, Dr. Yoshiyuki Sakai, the doctor who examined Yamato, told Asahi TV.
He spoke coherently and showed signs of mild dehydration and malnutrition; he had a light rash on his arms and legs, the doctor said.
The small building where Yamato was found is usually used as a rest station, but hadn't been used recently, Asahi reported. Yamato had wrapped himself up in two of the futon mattresses that were stored inside.
Odd circumstances
News of Yamato's disappearance spread beyond the island nation due to its odd circumstances.
The boy's father told authorities on May 28 that his son disappeared while picking wild vegetables with his family.
Tanooka later admitted they left him on the side of a mountain road in the woods of Nanae, home to wild bears. It was punishment for throwing stones at passing cars and people.
When his parents returned for him, the boy was gone.
Tanooka suggested the family hesitated to report him missing because of the punishment.
"I thought it might be taken as a domestic violence," he told TV Asahi.
The lie may have put search and rescue efforts at a strategic disadvantage, said the Fire Department's Saito.
"This is a very rare case, specifically with the story changing in the middle," Saito said earlier this week.
"We cannot speak retrospectively, but we would have seen a different development if we had known the story from the beginning."
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