Dom Richard Yeo, abbot president of the English Benedictine Congregation, said he believed the allegations of former residents who say they were abused at the fee-paying Highland boarding school, which closed in 1993.
But the Scottish Child Abuse Inquiry was shown a submission from the congregation which said it had “no remit or authority” to acknowledge or accept abuse.
The inquiry heard allegations have been made against six monks who taught at either Fort Augustus, on the banks of Loch Ness, or Carlekemp Priory School in East Lothian.
Dom Yeo said one monk, who was later accused of sexual abuse, was moved from the school but there was no evidence police had been informed.
He said his predecessors as abbot president had responsibility for ensuring that Fort Augustus was properly run, but he said that was not the same as having responsibility for its running.
Asked if he acknowledged abuse had taken place, Dom Yeo said: “Several people have come to me and informed me that they were abused and I have told them that I believe them and that I was sorry about it. That’s my position.”
He said he had agreed to take part in a 2013 TV documentary – in which a number of allegations were made – on the condition he was able to “say sorry for the abuse that happened”.
But when asked who could now be held accountable for the abuse, he said: “Since the monastery has closed, I don’t see how anybody can be.”
He added: “The great problem with all this is that Fort Augustus has closed down and that must mean that any redress that survivors of abuse have is going to be limited.”
Former pupils of Fort Augustus have made allegations of physical abuse, sexual assault and rape.
Prosecutors are currently attempting to extradite Father Denis “Chrysostom” Alexander after he was arrested in Australia.
Fr Alexander was among those accused of abuse in the 2013 TV documentary. He denies the allegations.
The Scottish Child Abuse Inquiry, before Lady Smith, is looking at the abuse of children in care dating back decades.
Yesterday it also heard from Vivienne Dickenson of Crossreach, the Church of Scotland’s social care council.
Ms Dickenson said the Church was “deeply sorry” for children abused while in its care.
The inquiry heard there had been a small number of historical allegations relating to the use of excessive force at Ballikinrain residential school near Stirling and two historical complaints of sexual abuse at Geilsland School, Beith, which closed in 2015.
In 2013, Ian Samson was jailed for sexual abuse that included attacks on children at the Church’s Lord and Lady Polwarth Children’s Home in Edinburgh, which closed in 1982.
Ms Dickenson told the inquiry Samson had been given a written warning after concerns were raised by another member of staff in 1980.
Commenting on the Edinburgh children’s home, she said: “We fully accept that the systems and processes did not protect children in our care at that time.”