A report by the organisation's committee for the prevention of torture called for "effective measures to address the lack of safety and high levels of violence" to be prioritised in both the youth secure estate and adult prisons. It also calls for the end of solitary confinement.
The report comes as a new body has been handed responsibility for commissioning and overseeing the youth secure estate from the Youth Justice Board (YJB).
The report said that while the committee welcomed the reduction in the number of juveniles detained in England and Wales from 2,905 at the time of its last visit in 2008, to 882 in March 2016, the reduction in numbers has resulted in a greater concentration of young people with the most complex needs being held in custody, notably in young offender institutions.
It said that between 2013 and 2015, there has been an increase in the number of assaults and deaths, including self-inflicted deaths of young persons in prison, three of whom were juveniles. It also notes that the increase in violence in the young person custody estate has come under sustained scrutiny and widespread criticism from a variety of stakeholders.
The committee has called for government to introduce urgent measures to "bring prisons back under the effective control of staff", and "reverse the recent trends of escalating violence, self-harm and self-inflicted deaths".
The committee said that, in light of the interim findings of the Taylor Review and the improvement board established following concerns about practice at Medway Secure Training Centre, which "underlined certain systemic weaknesses", there should be an urgent review of the current operating model of the young offender institutions and secure training centres.
The report added that this should be with a view to ensuring that, if, in exceptional circumstances, it is necessary to hold juveniles in detention, the secure juvenile estate is "truly juvenile-centred and based on the concept of small well-staffed living units".
It said the committee has visited a number of juvenile establishments in several countries, which are juvenile-centred and based on the concept of small living units, and would like the UK government to use these as the basis for planned reforms to the youth secure estate.
"These establishments are composed of small well-staffed units, each comprising a limited number of single rooms (usually no more than 10) as well as a communal area. Juveniles are provided with a range of purposeful activities throughout the day, and staff promote a sense of community within the unit," the report states.
"The CPT considers that this type of centre represents a model for holding detained juveniles in all European countries."
Carolyne Willow, director of children's rights charity Article 39, said: "This devastating report shows, once again, that vulnerable children are being held in intolerable prison conditions and they are suffering great harm. These are children in the care of the state or big businesses running prisons for profit.
"Penal practices and institutions should have long since been abandoned for children. As political parties busily prepare their election manifestos, it cannot be too much to ask that they each commit to close down child prisons and invest in interventions that have the child's wellbeing at heart. This is not only humane, it is basic common sense - you don't improve children's wellbeing, behaviour and home circumstances by locking them in a tiny, squalid room for 23 and a half hours a day."