More than 1500 juveniles went through the program during the last six months of 2012, with offenders and their families meeting with victims and a police officer.
It had a 99 per cent satisfaction rate, according to the children's court annual report.
Judge Shanahan said the reason for the decision to abolish the Youth Justice Conference was “unclear” to him, and said the program had a “substantial rehabilitative impact on young offenders”.
“If the reason was financial, then any savings in the costs of administering the conferences would, in my view, be illusory,” he said in the 2012-13 Children's Court annual report.
Responding to questions from Fairfax Media, Attorney-General Jarrod Bleijie did not answer a query about whether the government would consider re-instating the court-ordered program. However, he said Youth Justice Conference was still available through police.
In the annual report, Justice Shanahan said the program's demise would result in an increase in community-based supervision orders, which would be more costly and inflate the number of juveniles charged.
While police cautions dropped during 2012-13, charges laid against juveniles who appeared in court jumped from 21,535 to 26,186, an increase of 21.6 per cent.
However, the total number of offenders processed through the court system only rose by 10.1 per cent to 6,642. Of these, 85.8 per cent were found or pleaded guilty.