An unacceptable level of pain is being used to restrain children in secure custody, a report says.
The inquiry was launched after the death of Gareth Myatt, 15
The independent investigation into the treatment of children in prison, led by Lord Carlile, found pain was used to enforce compliance.
That was "unacceptable" and may be illegal, the report said.
The investigation was set up following the death of a 15-year-old boy in a privately-run secure unit while he was being restrained by three adult staff.
The inquiry, commissioned by the Howard League for Penal Reform, looked into the use of restraint techniques and strip searching.
It found that physical force was used against youngsters 15,512 times during a 21-month period in England and Wales, with injuries to both staff and children not uncommon.
Liberal Democrat Lord Carlile said his team of advisors "shared my shock at some of the practices we witnessed".
"We found that some of the treatment children in custody experience would in another setting be considered abusive and could trigger a child protection investigation."
Figures varied between institutions - in which there are in total 2,800 children and young people held in England and Wales, including 200 girls.
At one secure training centre, Medway in Kent, 1,818 injuries to children as a result of restraint from January 2004 to June 2005 were reported.
At Rainsbrook near Rugby there were 118, Hassockfield in County Durham reported 177 and Oakhill in Milton Keynes listed 48 from its opening in September 2004 to August 2005.
A sample of five out of 24 local authority secure children's homes in England and Wales revealed 73 injuries to children from January 2004 to August 2005.
Young offenders institutions did not keep central records of how many children had been injured in restraint incidents.
The inquiry found some evidence that staff would "bait" children into situations that would lead to them being restrained for the adult's "own gratification".
The level of pain used may be illegal, the report says
The report accepts that many of the 10 to 17-year-olds held in young offender institutions, secure training centres and local authority secure children's homes have had chaotic and abusive childhoods and lack clear boundaries to their behaviour.
But it said that unnecessarily painful restraint techniques were used to deal with dissent in some institutions.
Handcuffs were used in the four privately-run secure training centres, something the inquiry says should stop.
And the need for a strip search should be based on evidence, something the report says would cut the number of strip searches by half.
The Youth Justice Board chairman Professor Rod Morgan said staff were encouraged to use non-physical methods to deal with difficult behaviour.
"We want to move to a situation where the staff have sufficient confidence and are sufficiently well-trained that they don't have to rely on physical restraint to the degree that in some instances they are currently doing," he said.
However, he said there was an underlying problem about a lack of spaces for young offenders who had mental health problems - and should be in healthcare rather than custodial care.
He called for a three-part inter-departmental review - to look at children dealt with in the criminal courts and end up in custody; those dealt with in the family courts and end up in care; and those dealt with under the mental health act and end up in psychiatric care.
Children's Rights Alliance for England national co-ordinator Carolyne Willow, a member of Lord Carlile's advisory panel, said: "We are not talking here about children being hurt in the rough and tumble of restraint.
"Staff have permission to deliberately hurt children."
"As a former child protection social worker, I am stunned that this is allowed to happen."
The inquiry was told that one in five restraints of children resulted in injury.
'They're still children'
Director of the Prison Reform Trust Juliette Lyon says children are being failed by the prison system and they invariably end up re-offending.
Cases where children needed to be restrained should be the "rarest of rare events", she told BBC News.
"When you look at the number of times that physical restraints were used in the course of less than a year - thousands of times, on some quite young children - you realise it's being used as a matter of course when it's a disciplinary issue.
"Although children have behaved badly and some of them committed terrible crimes, although that is a minority, they're still children," she added.
Lord Carlile's report concludes that police should be ready to prosecute in cases where children appear to have been assaulted.
The inquiry was launched after the death of Gareth Myatt, 15, from Stoke-on-Trent, in April 2004.
He died after being restrained by three members of staff four days into his sentence at privately-run Rainsbrook secure training centre, near Rugby.