Jonathan Anderson, headmaster at Merchiston Castle School , said singling out boys-only schools in relation to the issue is "not fair".
Giving evidence at the Scottish Child Abuse Inquiry, Mr Anderson said the school - which charges nearly £12,000 a term for senior boarders – had undertaken the "harrowing" process of a full review of historic files and accepts there may have been abuse between 1930, when the school moved to its current site in Colinton, and 2014.
Counsel to the inquiry, Andrew Brown QC, questioned him on recent media reports of a "predatory culture" that boys' schools can produce.
Mr Anderson, who took up his role at Merchiston in 2018 after a 20-year career teaching at boarding schools in England, said: "I think it is an issue across all schools.
"I think it's unfair to single out boys' schools as I think it's a societal issue.
"I think it's about how we educate young men, and we take that responsibility very seriously.
"Being able to have a frank discussion with them in a boys-only space is very healthy in that regard.
"To say it's only an issue for boys' schools is not fair."
The inquiry also heard from a written statement from the school which said the review of records found it had failed to protect some children from abuse, in particular in relation to a now-dead member of staff.
The review found there may have been physical and emotional abuse at the school over the nine decades examined - including bullying, voyeurism and "lewd practices".
The records point to this mainly involving staff abuse of pupils but the files also contain references to verbal and physical bullying among students.
One account from a pupil in the 1950s describes both sexual abuse and bullying from students.
Further documents indicate in the past that the school - the only remaining boys-only independent boarding school in Scotland - had not adequately recorded all reports of abuse.
Mr Anderson said: "It has been a salutary experience and a harrowing experience for all involved and we are deeply sorry that it's taken this to bring it to our attention but the school of today absolutely recognises that safeguarding is our top priority."
The inquiry heard the school has updated its child protection policies, trains both pupils and staff on this and has increased oversight on the issue.
Mr Anderson added: "We have absolutely learnt from process. Safeguarding is our number one priority and the wellbeing of the young people in our care is of uppermost importance to us."
Rodger Harvey-Jamieson, a former clerk to the board of governors at the Keil School in Dumbarton, which closed in 2000, also gave evidence on Tuesday.
He said nothing was reported to them or the school founders, the Mackinnon-Macneill Trust, of which he is a trustee, about concerns over staff members until they heard of a police investigation.
"It was a complete shock to the system to discover that there had been failures which allowed abuse to take place," he said.
The trust acknowledges that between 1997 and 2000 some children suffered abuse at the school.
"We had absolutely no inkling or suspicion that that sort of abuse was going on at the school. It's devastating that it should've taken place," he said.
"Again, I want to offer our profound sympathy to all who have been affected by this."
The inquiry, being heard before Lady Smith in Edinburgh continues.