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The boy sparked a police search when he left his mother's house in Ocean Grove, Dunedin, before boarding a bus at about 4pm Thursday and travelling across the city, bound for his father's place in North Dunedin.
He was found at the house, near the Woodhaugh Gardens area about 9km away, about two hours later.
It is understood the boy, who frequently ran away, decided he wanted to see his father.
Determined to get to his father's house across town, he walked out of the Luke St home and down to the nearby bus stop in Tomahawk Rd.
There he boarded the No3 (Ocean Grove-City-Ross Creek) bus and offered the driver a $5 note, but the driver declined the money, saying he could ride for free.
He rode all the way to North Dunedin before getting off the bus, visiting a dairy to spend his money, then eventually wandering to his father's house. His father immediately contacted relatives to assure them the boy was safe and well.
Otago Regional Council support services manager Gerard Collings said he had spoken with the service operator Go Bus, which explained the child had boarded at the same time as another adult, indicating the driver may have mistakenly believed the two were travelling together.
"That's where the confusion started."
The child appeared familiar with the bus network, and also looked a little older than his five years, he said.
"The child is obviously very conversant with the system, knows how to use it.
" ... the child appeared to have been a little bit taller than the average 5-year-old."
Mr Collings said the driver was in a difficult position, as he could hardly leave the 5-year-old standing at the side of the road.
"It's an extremely difficult one ... our buses are used by school children all the time."
However, the ORC would be reviewing its policies and processes together with bus operators in the new year to insure a "consistent approach," he said.