Children 1st, which works with those affected by abuse in Scotland, said a police investigation into historic allegations at Fort Augustus Abbey School in the Highlands may not be enough to address victims' concerns.
The charity has also called on the Catholic Church to fully co-operate with the ongoing investigation and for it to pass on any information it has to the police.
More than 50 former pupils of the school and its preparatory school Carlekemp in East Lothian, which have now closed, came forward last month with allegations of ill-treatment at the hands of monks from the 1950s to the 1990s.
Ten monks have been accused of physical abuse and four monks and one lay teacher face claims of sexual abuse, including the rape of a schoolboy.
In addition, three headmasters stand accused of covering up the scale of the abuse.
Chief among those identified is Father Aidan Duggan, an Australian monk who taught at Fort Augustus between 1953 and 1974, who is accused of grooming young boys during piano lessons.
Father Duggan died in 2004, but some abuse claims relate to men who are still alive.
The children's charity, NSPCC, has called for a full independent inquiry.
Children 1st Chief Executive Anne Houston has now added her voice to the calls.
She said: "Where there are worries the police investigation won't address victims' concerns as the accused are now dead, we would support the need for an independent inquiry, as long as the expectations of what it could achieve for both the adult victims and for children now and in the future is clear at the outset.
"The focus here must always remain on what's best for those who were abused in the past and what will make a positive difference to them; that and helping protect children now and in future by taking steps to minimise the risk of this ever happening again.
"It is crucial that the church fully and openly co-operates with the ongoing police investigation and passes on any and all relevant information it may have relating to any allegations of abuse at these schools.
"It would be actively unhelpful to set up expectations that cannot be met and could serve to make those abused feel further let down."
The charity runs a dedicated abuse support line staffed by trained volunteers to offer emotional and other support to victims of abuse.
Hugh Gilbert, the Bishop of Aberdeen, has apologised on behalf of the Catholic Church for the Fort Augustus scandal, as has the Benedictine order which ran the schools.
Speaking to parishioners earlier this month, Bishop Gilbert said that the abuse was "a most bitter, shaming and distressing thing".
On Wednesday, Father Francis Davidson, a former headmaster at the school, resigned from his senior role at a college of Oxford University.
He has quit as monastic superior of the Benedictine college St Benet's Hall, where he was responsible for the welfare of student monks at the university.
Father Davidson is accused of covering up child abuse during his time at Fort Augustus Abbey School in the Highlands.
As the only surviving headmaster of the school, he offered his sympathies to former pupils and their families and said he was shocked and saddened to hear the allegations.
However, he said he did not recall them being reported to him during his time in charge.
A spokesman for Police Scotland said the investigation was ongoing.
Carlekemp closed in 1977 and Fort Augustus Abbey School was shut in 1993.