There had been some success in accelerating the time from arrest to sentencing, but the new bodies had "struggled" to tackle underlying, complex social problems in the lives of young offenders.
Nearly all the targets relating to youth education, training, employment, drug abuse, mental health and accommodation had been missed, concluded the authors.
The YJB's latest figures show youth crime is broadly stable but with a recent rise in recorded offences involving girls.
Reoffending rates remained highest among those who had a custodial sentence - but lower for those dealt with before reaching court.
Enver Solomon, co-author of the CCJS report, said the findings suggested the multi-agency youth offending teams were not necessarily working.
"The government's record on youth crime and tackling the multiple needs of children caught up in the youth justice system is less impressive than many would have expected," he said.
"This raises questions about the success of the reforms in making an impact on the number of children and young people who offend, and demonstrates that the youth justice agencies can do little more than regulate youth crime.
"The government has placed too high expectations on the youth justice system and should be clearer about its limitations."
The YJB dismissed the report, saying it had failed to acknowledge significant improvements such as a cut in reoffending over five years.
I'm afraid the government have run out of road. We used to hear about their respect agenda. That's gone now
The board said it was on course to meet a 2008 target to reduce the number of young people being brought before the youth justice system for the first time.
"The Audit Commission review in 2004 reported the system was a considerable improvement to the old one and that improvements have continued," said Frances Done, chair of the board.
"We deal with some of the most troubled and troublesome children in the country - there is no simple or easy solution - but great strides have been made in the community and in custody to hold young people to account for their actions and to protect the public."
Shadow Justice Minister Nick Herbert said the report showed the government's policy had failed.
He said: "I'm afraid the government have run out of road. We used to hear about their respect agenda. That's gone now.
The report's author discusses solutions to the problem
"We have a prime minister who hasn't made a speech on crime since he took office, which I find simply extraordinary, given public concern about this issue."
Barnardo's chief executive, Martin Narey, said the biggest concern was the increase in the use of custody on young criminals.
He said: "The fundamental issue remains the over use of custody for children who have not committed violent offences. Until this is addressed both the youth justice and welfare systems will continue to fail some of our most damaged and vulnerable children."
A Ministry of Justice spokesperson said the government was committed to intervening early with young people to prevent crime.
He said: "Much has been achieved in tackling youth crime. Reoffending among juveniles fell by more than 17% between 2000 and 2005 and overall youth offending levels remain stable.
"However, there is clearly more work to do and we are pushing forward our efforts to reduce reoffending further, including by launching a Youth Crime Action Plan this summer."
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