Appearing outside the hospital the boy was taken to after he was found, his father apologized and vowed to do a better job of raising him.
A military officer, speaking on the national broadcaster NHK, said the boy was found when a soldier unlocked the hut, about five kilometres from where he disappeared.
The boy told police he had been in the drill area for several days after walking alone in the forest.
The boy suffered some dehydration and was getting an intravenous drop, but besides some minor scratches on his arms and feet, no serious risks to his health were found, a medical doctor who had examined him was quoted as saying by Kyodo.
More than 180 rescuers, including troops, had been searching the area.