The report by HM Chief Inspector of Prisons for Scotland, David Strang, found there was no regime in place at HMP and Young Offenders Institute Grampian for a small number of inmates being protected for their own safety.
Mr Strang said the situation was “unacceptable”, with some offenders feeling they were being “punished” for going into protection.
The inspection also found that no young men have been held at the Peterhead prison since a riot involving young offenders shortly after the £140 million facility was opened in 2014.
There were 431 prisoners held at the prison – which has a capacity of 506 – during the inspection late last year.
The removal of male young offenders meant one of the residential halls was unoccupied.
Mr Strang said it was “disappointing that some of the highest quality of prison estate in Scotland lies empty”.
According to the report, those deemed “non-offence protection prisoners” often spend almost the entire day in their cells.
The category includes prisoners who have asked to go into protection due to fears over their safety often linked to drug debts and disputes.
Mr Strang said: “Non-offence protection prisoners spoken with felt they were being punished for having asked to go on protection. They explained that there was no regime for non-offence protection prisoners so they could end up spending 23 hours a day in their cell. This was confirmed by staff. This was unacceptable.”
Mr Strang said the same prisoners were only allowed to exercise one person at a time in “pens” attached to the Separation and Reintegration Unit (SRU), further reinforcing their “social isolation”.
A spokeswoman for the Scottish Prison Service said: “HMP & YOI Grampian provides opportunities for non-offence protection prisoners to access education and training should they wish to attend.
“Learning centre staff also visit these prisoners in their hall to provide educational opportunities. These prisoners also have the opportunity to attend visits, access chaplaincy services and have daily recreational opportunities.”