Pupils at schools linked to a religious order were “robbed of their childhoods” by the physical and sexual abuse which took place there, an inquiry has heard.

Paul Reid, representing the English Benedictine Congregation, said it had “taken too long” for the pupils affected to be heard and believed.

His comments were made during closing statements in the latest phase of the Scottish Child Abuse Inquiry.

It has been investigating schools linked to the English Benedictine Congregation, particularly Carlekemp in North Berwick and Fort Augustus Abbey in the Highlands.

The inquiry has heard that one former teacher at Fort Augustus Abbey, Thomas Seed, known as Father Benedict, was found guilty last year of physical abuse against a pupil at the school while extradition proceedings are ongoing in Australia and Canada regarding other abuse allegations.

Mr Reid told the inquiry in Edinburgh: “The core truth remains that pupils at Carlekemp and Fort Augustus Abbey were subject to abuse and a schooling which robbed them of their childhood and has caused lasting damage to them and their families.

“The English Benedictine Congregation regrets very much this was able to happen in schools in membership of the congregation.

“It has taken too long for them to be heard and believed and the congregation is sorry this has been so and repeats its unreserved apology to all affected.”

Colin MacAulay QC, senior counsel to the inquiry, told the hearing: “If the main body of evidence is accepted, then there were brutal regimes involving excessive punishment at both Carlekemp and Fort Augustus Abbey.

“There was evidence that bullying was prevalent and indeed tolerated … and a body of evidence implicating Carlekemp and Fort Augustus Abbey in the sexual abuse of children.”

He told the inquiry this covered decades at both schools as he highlighted the movement of monks between schools and overseas.

Mr MacAulay  said it was “difficult to believe that the monks did not know that children were being sexually abused at both schools”.

John Scott QC, representing the In Care Abuse Survivors (INCAS) group, said: “The congregation either didn’t know what was going on, in which case they failed in their observing role, or they knew but took no action, in which case they were complicit in covering up abuse.

“The true answer might be a bit of both.”

He added: “It may be that the clear evidence of known and suspected abusers being moved on is one of the worst aspects.”

He said witnesses spoke of abusers being moved to other church roles in Canada and Australia, with one describing it as “pass the paedophile”.

He said this was at times “suggestive of a network” and added:  “It is little wonder that people see the church as having involved paedophile rings, crossing monasteries, crossing borders and crossing continents”.

The inquiry in Edinburgh begins a new phase on Thursday focusing on the Marist Brothers.