Police on horseback were among 130 rescuers scouring a mountainous area of the northernmost island of Hokkaido from dawn for Yamato Tanooka, who went missing on Saturday.
His parents first said he had disappeared while the family foraged for edible plants. They later told police they had left him by the road to discipline him after he threw stones at people and cars.
They said they drove about 500 metres (yards) down the road but when they went back a few minutes later he had disappeared.
The area is so remote that residents of the region say they rarely go through it.
“We have done an unforgivable thing to our child, and we have caused a lot of trouble for everyone,” Yamato’s father, Takayuki Tanooka, told television reporters.
“I just hope he is safe.”
Thousands of people took to social media, some to pray for Yamato’s safety in an area where the temperature at night falls to 7 Celsius (45 Fahrenheit).
Heavy rain is forecast for Tuesday night and the boy was wearing only a T-shirt and jeans.
“When I think of him being alone in the woods like that, my heart aches,” said one person posting on social media.
But most people on social media rebuked the parents as neglectful.
“If he was actually throwing stones at cars, that shows there wasn’t a lot of discipline anyway – and probably not enough love either,” said one person.
“Whatever the result, this is parental neglect. It’s cold in the Hokkaido mountains, and I hear there are bears, too,” said another person.