Andrew Ong, 11, was found by himself at Melbourne Central train station by protective service officers about 7.30pm on Monday following a frantic hunt by police and his parents.

The boy left a five-page note on the kitchen table before taking his myki and a backpack and fleeing from his parents' home in Carramar Avenue, Camberwell, about 8.35 on Monday morning.

A police spokeswoman confirmed Camberwell station police had sent a car to collect Andrew from Melbourne Central and reunite him with his family.

Andrew had got into minor trouble at Hartwell Primary School, and felt ashamed about disappointing his parents, his mother, Cindy Ong, told a media conference.

"He's very upset with himself, and that's why he's taken off. We just want him to know it's OK, he's not in any trouble, just to come home," Mrs Ong said.

"He left a note lying on the table about why he's doing it, about how he feels sad about what has happened at school. He just wanted to have some time to think. And he'll come back Friday. I think he was just feeling a bit daunted about coming back to school, and that's why he's taken off."

Midway through the press conference at Camberwell police station police handed Mrs Ong a photo taken from a camera at Willison Station in Camberwell shortly after 8.30am.

"Oh my god. He brought his jacket. That's him," she said.

The picture showed Andrew on the city side of the station, confirming his parents' fear he may have used the myki to travel into the CBD. They, along with police, spent the day searching the local area and the city. They also searched ACMI, where Andrew sometimes goes to play video games.

He took some pocket money and his myki but no food supplies, his parents said.

Mrs Ong said the school dispute was over canteen duty.

"Kids were being silly. They were giving treats to their friends. And the principal made them write a letter. So I think he feels really bad about what he's done. He probably feels that we're disappointed in him."

Police thanked the public for their assistance.