Alone in the forest, the child had no food or water and has endured heavy rains at night, according to AFP.
It only took several minutes for Yamato Tanooka to vanish after his parents abandoned him by the side of the road to teach the misbehaving boy a lesson.
By the time his parents came looking for him, the child was missing.
"The parents left the boy in the mountains as punishment," a police spokesman told the Japan Times. "They said they went back to the site immediately, but the boy was no longer there."
Hokkaido police said the child went missing at the weekend. Two hours later, the boy's parents called police and told them that the child had disappeared on a day trip while the family scavenged for wild vegetables, CNN reported.
Takayuki Tanooka, the boy's 44-year-old father, eventually admitted that the family's story was fabricated and that his son had actually been left behind as punishment for throwing rocks at cars along a road in the area, the Japan Times reported. Tanooka told a local reporter that he could not initially admit to authorities what he had done, according to the paper.
"I was not able to ask for [a search] with a reason of punishment," he told TV Asahi, according to CNN. "I thought it might be taken as a domestic violence."
Police said a search party of more than 150 officers and firefighters has been looking for the boy, who was wearing navy shorts, a black pullover and red sneakers at the time of his disappearance, according to CNN.
The northern side of the road on which the boy was left slopes toward Mt Komagadake, which rises just over 1127m, according to AFP.
"Unless he started climbing the mountain, he would have hit a main road after walking for 2-3km in any other direction," Saito told AFP.
Video footage shows dozens of searchers tramping through dense forest and thick foliage while a helicopter buzzes overheard, according to AFP. Rescuers moved through the search zone holding torches and calling out the boy's name.
"I feel very sorry for my child," the father told an NTV reporter. "I am so sorry for causing trouble for many people."
The area where the child was last seen is home to wild bears, according to the Times.
Mitsuru Wakayama, a spokesman for the nearby town of Nanae, told the Times that the area is used as a shortcut by locals - but not often, because of how precarious it can be.
"Not many people or cars pass by, and it gets totally dark as there are no lights," Wakayama said. "It's not surprising to encounter bears anywhere in the area."
With police still deciding whether the parents will face charges related to child abandonment, many critics are calling for the parents to face repercussions, according to the Times.
"This is not punishment but abuse!" one Twitter post read.
"The parents are so stupid that I am speechless," another said.
AP reported that the boy's father expressed remorse in an interview with the public broadcaster NHK and other TV stations: "I regret what I did to my child," he said.