Tam Baillie’s comments follow allegations that a third Australian monk was part of a suspected paedophile ring at the school.
The Scottish Government has insisted so far that the allegations were matters for the Catholic Church in Scotland, and were for Police Scotland to investigate.
But Mr Baillie, commissioner for children and young people, said that in light of the widening extent of the abuse, the government should set up an inquiry.
Speaking yesterday, he drew parallels with the abuse scandal surrounding Jimmy Savile: “I am actually appointed by parliament, not by the Scottish Government, and the Government has to listen to the lobby, if you like, the views, the judgment – and in my judgment this requires an independent inquiry.
“There are echoes here of what is happening down south with regard to Savile and the number of inquiries that has spawned, and there are even more distant echoes of what happened in Ireland in the 1980s and 1990s.”
The abuse was reportedly carried out by monks over several decades at Fort Augustus and its preparatory school in East Lothian, Carlekemp, both of which are now closed. The scandal which is believed to have involved at least 50 victims, and the surrounding cover-up was revealed in a BBC investigation broadcast last month.
Mr Baillie’s comments came in the wake of further revelations relating to the controversy. One of the school’s headteachers, Father Francis Davidson, announced on Wednesday that he was stepping down as monastic superior of St Benet’s Hall, where he was responsible for the welfare of student monks at the Oxford College, in the wake of direct accusations that he covered up abuse.
On Thursday, four former pupils named a third Australian monk in the child abuse scandal.
Two men, Fr Aidan Duggan and Fr Chrysostom Alexander, had already been accused of being paedophiles, but Fr Fabian Duggan, Fr Aidan’s brother, was added to the list of abusers.
However, on Friday last week, the same day that the allegations were put to Fr Fabian and the Sydney Catholic Church, he died, aged 83.
All three Australian monks left Fort Augustus in the 1970s.
Meanwhile, also on Thursday, Danny Sullivan, chairman of the Catholic Safeguarding Commission in England and Wales, said the Church in Scotland would benefit from outside scrutiny and criticised Bishop Joseph Devine, the retired bishop of Motherwell, who has dismissed calls for an independent inquiry.