"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."
Despite the larger search party no leads turned up, with many worrying the boy might not have survived heavy rains which fell on Wednesday. He was last seen wearing a T-shirt and jeans in an area where the overnight temperatures can fall as low as 7C.
The search has gripped Japan, with news programmes offering hourly updates, and thousands have taken to the internet to both pray for the boy's survival and excoriate his parents for what is seen as neglect.
"If I was a small child in this situation I would either run after the car or wait there until they came back. I just hope he is safely found," one person wrote.
- Reuters