Children at a private boarding school were let down by decades of “systemic failures” with house masters free to rule their own “fiefdoms” without oversight, an inquiry has been told.

Between the 1950s and 1990s in particular, boarding pupils at Morrison’s Academy were exposed to school rulers who could discipline them by “whatever means deemed allowable by that house master”, the Scottish Child Abuse Inquiry heard on Thursday.

The inquiry has heard evidence of pupil-on-pupil sexual abuse as well as physical beatings and emotional torments endured by children at the school in Crieff, Perthshire, which was established in 1860 and was a boarding school until 2007.

On Thursday, its current rector Gareth Warren repeated the school’s “genuine and heartfelt apology” and agreed there had been decades of “systemic failures” in safeguarding children.

He agreed with inquiry counsel Andrew Brown QC that between the 1950s and 1990s across several different boarding houses “there seemed to be fiefdoms in operation with, in effect, no oversight at all”.

Mr Warren, who is to become principal at George Heriot’s School in Edinburgh after six years at Morrison’s, said he recognised the “courage it has taken for applicants to come forward and give their evidence”.

He told the inquiry: “The very clear emerging theme right through is that the culture in certain boarding schools was one of delegation of duty to instil discipline and order in boarding houses by whatever means deemed allowable by that house master.”

He said delegating discipline had been an “abdication of duties” by schools at the expense of the wellbeing of children.

“That manifested very much in physical abuse and underlying that was emotional abuse, having constant fear about what might happen next,” he said.

The inquiry has heard from former pupils of Morrison’s, including one who was sexually abused by an older pupil for four years and suffered beatings so frequent his “buttocks were always bruised”.

Others recalled teachers taking “delight” in caning children and how one boy was beaten so severely his wrist was broken.

Alasdair Liddle, who joined Morrison’s in 1950, said he was tormented by a more senior pupil who threatened to brand him with a red-hot poker and stubbed out a cigarette on his bare skin.

Another, now in his 70s, said beatings endured from an “extremely violent” teacher “still disturb me” more than half a century later.

The inquiry, before Lady Smith, continues next week.