Tanooka, 44, said his son had been throwing stones at cars and, as a punishment, he and his wife got into their car and drove off.
They stopped the vehicle less then half a mile away and walked back to where they had left the boy, but he had disappeared.
Tanooka told police he was gone for about five minutes.
In an interview with TV channel Asahi, he added that he did not dare tell the truth when he asked the police to initiate a search for his son. It is not clear whether the boy's parents will face charges.
Brown bears can be extremely aggressive and two men have been killed in bear attacks in northern Japan already this month.
In separate incidents in Akita Prefecture, two men were attacked and killed while they were picking wild bamboo shoots. The bodies of both men had extensive bite and scratch marks.
An adult Ussuri brown bear can grow up to 550kg and there are an estimated 3000 such bears in Hokkaido.
The prefecture was also the site of the worst bear attack in Japan, when an Ussuri brown bear attacked villagers in Sankebetsu, killing seven people over the space of six days in December 1915. It was subsequently shot dead and found to weigh 340kg and was about 2.7m tall.