A report based on surveys of young people in custody conducted by the standards watchdog in 2015/16 found that 46 per cent felt unsafe in young offender institutions (YOI) - the highest proportion since the prisons inspectorate began surveying those in youth custody in 2001.
The figure for secure training centres stands at 23 per cent.
The report reveals that around one in three children and young people reported being specifically victimised by being shouted at through windows.
The findings come in the same year two YOIs were handed damning inspection reports criticising high levels of violence among young offenders.
In September prisons minister Sam Gyimah was asked to outline what is being done nationally to reduce levels of violence in youth custody, after it emerged there were 19 instances of grievous bodily harm in a single establishment in the space 12 months.
In March, then Justice Secretary Michael Gove pledged that action would be taken to tackle gang problems and improve safety in youth jails.
Peter Clarke, chief inspector of prisons, said that over the past year only one YOI has been considered safe, adding "these poor outcomes in safety are directly related to correspondingly poor outcomes in education" among inmates.
He said other concerns to emerge from the thematic report emerge is the "disproportionate over-representation" of certain groups.
In YOIs 47 per cent of boys are from black or ethnic minority backgrounds, while the proportion in STCs is 41 per cent.
In addition, 19 per cent of those in YOI's have a disability and 22 per cent describe themselves as Muslim. In STCs 12 per cent are from Gypsy, Romany or Traveller backgrounds.
"I hope these findings are taken seriously by those charged with developing and improving policy," Clarke said.
The survey involved findings from 767 questionnaires and was commissioned by the Youth Justice Board (YJB).
Colin Allars, YJB chief executive, said parts of the report are "uncomfortable to read", adding that "trends around safety are concerning".
"We will use these findings to support our work with providers of custodial services to address the issues children and young people are telling us about," he said.
Frances Crook, chief executive of the Howard League for Penal Reform, said concerns raised by some of the 330 young people in custody who called its legal advice service in the last three months include poor treatment by staff and lack of planning around their release.
She said: "Our youngest caller was 15 and the youngest person we received a call about was 13. The children need help with cruel punishments like being held in solitary confinement for weeks on end, poor treatment and the prospect of being released destitute."
"It is shameful that the government spends millions on locking up children yet they are unsafe inside and lack support before and after custody. The prisons are a disgrace and should be closed," she added.
