Justice Lex Lasry said the boy - who is facing charges including possession of cannabis, car theft, criminal damage, breaching bail conditions, unlicensed driving, theft and burglary - was no criminal.

The boy had earlier been in tears asking to be bailed to go back to his family who did not want him.

"His heart's breaking because he's lost his family," Justice Lasry said. "The community expects that young boys in this turmoil will be looked after. And he's not being looked after."

The judge said the boy's bail application appeared to underline some failures in the system.

"The applicant for bail ... is aged 13 and is clearly a boy in need of significant assistance. That need for assistance is urgent," he said.

"Our community has an obligation to help young people like [the boy] to get back on their feet and to solve these problems.

"The problems confronting [the boy] are social and family problems. He is not a criminal.  He is charged with criminal offences but at 13 years of age he is not a criminal and he shouldn't be treated like one."

The boy had been held in a youth detention centre for 26 days when he appeared before Justice Lasry.

A Department of Health and Human Services officer said the boy's mother was living with his two older siblings but was refusing to have him back, saying she could not handle him and did not want him running way.

The boy's father was living in Queensland and had cut off all contact with him.

Asked by the judge if foster care was an option for the boy, the DHHS officer said the department had a lot of difficulties getting foster carers to look after adolescent children "and there just isn't any".

The DHHS officer said it was the department's hope that the mother would eventually agree to care for the boy.

Justice Lasry said he wanted something done to help the boy, "otherwise his life is just going to turn in to a permanent state of misery".

"He obviously needs some kind of youth psychology assistance, he needs to be counselled, he needs to be supported, probably on a daily basis. You can see the distress he's in."

A Victorian Legal Aid lawyer told the court the only alternative to keeping the boy out of the youth detention centre was to transfer him to a residential unit but he had already absconded from there a number of times because he wanted to be back with his family.

Given the lack of available options to house the boy, his bail application was eventually withdrawn and the case adjourned to the Children's Court next Monday.