HM Inspectorate of Prisons for Scotland (HMIPS) was asked to carry out the work following the deaths last year of William Lindsay, 16, and Katie Allan, 21.
The report highlighted a “lack of proactive attention” to the needs, risk and vulnerabilities of those on remand and in the early days of custody.
And it identified “systemic inter-agency shortcomings” in the way information is shared across the justice system, inhibiting the management and care of young people.
William, who was being held on remand, took his own life within 48 hours on being placed in Polmont, despite being flagged as a suicide risk.
An evidence review carried out for the HMIPS report found Scotland consistently has a higher prison suicide rate than England and Wales, with the number of inmates taking their own lives on the rise.
It also found that more than two-thirds of suicides of young people take place within three months of the person being detained.
The report made a total of 80 recommendations and seven key recommendations, including the minimisation of social isolation during the early weeks in custody and the introduction of a bespoke suicide and self-harm strategy for young people.
HM Chief Inspector of Prisons for Scotland, Wendy Sinclair-Gieben, said: “Firstly, HMIPS would like to offer our sincere condolences to the family of Katie Allan and William Lindsay, whose deaths gave rise to this expert review.
“It is important to note that this review explored the wider issues of young people entering custody; we were not asked to consider the specific circumstances or details of individual cases.”
She added: “What has become clear in the evidence review and accompanying academic research is that being traumatised, being young, being held on remand and being in the first three months of custody increases the risk of suicide.”
The parents of Katie Allan welcomed the review, but said an inspection report, also published yesterday, which described Polmont as a “leading-edge prison” was “delusional and desperate”.
Linda Allan said: “We appreciate that there has been a great deal of work that has gone into the mental health review which involved a number of supporting organisations and in a short period of time.
“However we are deeply disappointed by the HMIPS inspection report, which we see as a missed opportunity and a desperate attempt to cover up the Scottish Prison Service’s (SPS) failures which led to our daughter Katie taking her life.”
Scottish Labour said the report showed young people are being “let down” by the prison system, while the Lib Dems described the situation as a “mental health emergency”.
Justice secretary Humza Yousaf, who asked for the review to be carried out, said: “We take the mental wellbeing of people in prison very seriously and while the numbers of suicides by young people in custody are small, no death should be regarded as inevitable. Any suicide in custody is a tragedy that has a profound effect on family and friends, as well as prison staff, and my thoughts are with all those who have lost loved ones to suicide.”
A SPS spokesman said: “The safety and wellbeing of everyone in our care continues to be a priority for SPS and work is already underway to strengthen the support available.”