The number of children in custody who are restrained has more than doubled in the last five years, according to research.
A report by the Howard League for Penal Reform on the use of restraint, solitary confinement and strip-searching in child units in England and Wales describes the practice as the "illegal, systemic physical abuse of children in prison".
The latest research also shows that children have suffered 4,350 injuries in the last five years while being restrained.
Frances Crook, chief executive of the Howard League for Penal Reform, said children in custody are "mistreated, abused and suffer a punishing regime".
The report comes 10 years after the Carlile Inquiry recommended that restraint should never be used as a punishment or to secure compliance.
The original inquiry followed the deaths of two boys in secure training centres, and the latest report, the Carlile Inquiry 10 Years On, looks at what progress has been made.
The Howard League for Penal Reform said the report shows restraint is widespread in young offender institutions and accounts for 22% to 34% of all times force is used on children.
In one incident in Cookham Wood prison, Kent, a boy was restrained for refusing to leave a room after a review into whether he was at risk of harming himself. Inspectors found that force was instigated quickly and escalated to an officer causing the boy pain by kicking him.
The report found that children are no longer being routinely strip-searched but some are still being held in solitary confinement.
The most recent survey of children in prison found that more than a quarter of boys had been held in segregation units at some point.
The research comes after a damning BBC Panorama expose allegedly showed staff mistreating and abusing young inmates, and boasting about using inappropriate techniques to restrain children at Medway Secure Training Centre in Rochester.
Lord Carlile of Berriew QC, who led the original inquiry, called on the Ministry of Justice to do more to implement his previous recommendations.
He said: "It is time that the Government recognises that the use of force on children, simply to make them do what they are told, is both unacceptable and unlawful.
"A healthy response to children in trouble with the law, which has their welfare at its heart, would recognise this use of violence by adults as an admission of failure."
The Ministry of Justice insisted the safety and welfare of young people in custody is its "highest priority" and that restraint and segregation should only be used as a last resort when there is no risk of harm.
A spokesman said: "We are clear that if restraint is absolutely necessary, it must be used within the parameters of the law, and comply with strict safeguards.
"We have also introduced a new system designed to minimise the use of physical restraint in youth custody and we are committed to improving practice further.
"We have also asked Charlie Taylor to conduct a review of youth justice. He will report back in due course with recommendations on how to improve the treatment of young people in our care."