In his annual report published last week, Dr Andrew McLellan called each of the 18 under-16s he found in Scottish prisons over the past year a "stark illustration of the cost of failure".
Most were held at Polmont Young Offender Institution, but others were held in adult jails, for periods of up to 155 days.
"However enlightened the regime, a prison is likely to harm children," wrote McLellan. "They will be held in isolation, or they will mix with older people."
A Scottish Executive spokeswoman said the number of children held in Scottish prisons had fallen since 2002. She said: "The vast majority of those held are children on unruly certificates, whose behaviour is so challenging that a sheriff has deemed them to be at risk to everybody's safety, including their own."
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