Peter Brodie, rector of Glasgow Academy, yesterday received an official reprimand from teaching's ruling body for the incident.
In an unprecedented case, Brodie was brought before a disciplinary panel of the General Teaching Council for Scotland (GTCS), after the parents said their son had been left psychologically damaged.
It is thought to be the first time a headteacher at a prominent school in the private sector has faced such a hearing.
The ten-year-old boy was removed from the playground at lunchtime on 29 August last year and grilled after a classmate accused the boy of supplying him with a cannabis joint.
Eventually, the mother was called at around 4pm and arrived at the school find the boy "crying uncontrollably" after an hour and 45 minutes of interrogation by the rector and head of the primary school.
Although the school's ruling board of governors agreed this was too long, and the boy was innocent, they refused to take any sanction against the rector.
Yesterday, Brodie pleaded guilty to a charge of interrogating the pupil on criminal allegations without allowing him to be represented and supported by an adult.
Robbie Burnett, lawyer for the GTCS, said: "The right thing would have been to have contacted police and get social work involved and, certainly, to have contacted the parents.
"It was inappropriate to take the young boy from the school playground into a position of interview lasting an hour and 45 minutes. Five minutes was all that was required."
Brodie's lawyer, Tim Glover, admitted 20 minutes would have been long enough to get the facts, but defended his client. He said: "Mr Brodie is an experienced professional with in excess of 30 years teaching experience. He was faced with an incredibly difficult situation – there were rumours going around the school of drugs being introduced into the school."
However, Mr Burnett demanded sanctions against the rector. He said: "It was wrong for Mr Brodie to have interviewed the ten-year-old boy for this length of time.
"It showed remarkable lack of judgment. It may be that it is regarded as an error on his part, but it was a grave error which shouldn't have happened."
The disciplinary sub-committee ruled that a reprimand be placed on Brodie's record for five years and that his employer be informed.
Jim Thewliss, chair of the sub-committee, said it also strongly recommended that Brodie undergo a course on interviewing children.
The boy's father said they were grateful to the GTCS for taking up the case but they did not rule out further civil action.
He said: "The GTCS decision has shown that independent schools cannot take the law into their own hands and we feel that justice has been done.
"We assume that the governors will now issue another letter to all parents advising them of Mr Brodie's guilt.
"The decision has given us closure on this episode and we now want to put it behind us."
No-one was available from the school's board for comment.
Analysis: One law for state schools, another for private
THE law dictates all teachers must have a valid teaching qualification and be registered with the General Teaching Council for Scotland (GTCS) which acts as both the professional body for teachers and also as its police force.
Anyone who hurts children, is convicted of a criminal offence, or even someone who is a poor teacher, can be struck off the register and banned from teaching in any classroom.
The aim is to prevent pupils from being exposed to abusers, thieves and bad educators.
However, this only applies to state schools, not private schools.
Although most in the independent sector do insist upon registration, official statistics show only 86 per cent of teachers in Scotland are registered, leaving around 480 independent school teachers who are not.
The anomaly means any judgment by the GTCS can be ignored by any private school.
The family in yesterday's case had wanted to take the head of Glasgow Academy's prep school, Tony Brook, to the GTCS as well.
However, as he was unregistered at the time, they were powerless. He has since said he intends to register.
Judith Gillespie, policy development manager with the Scottish Parent Teacher Council, said parents in state schools have more power.
She said: "They have more rights and much more influence because they can appeal to the local authority and ask for change."
The GTCS has already asked for the law to be changed to give them power over the independent sector too.
A consultation document by the body written earlier this year says it should have the same power to uphold standards in all schools.
It said: "Recent experience has shown that there is a significant loophole in those cases where a non-registered teacher in the independent sector is found to be incompetent or to have behaved unprofessionally."
A Scottish Government spokesman yesterday said it supported efforts by the GTCS and private schools to increase the level of registration.
However, he added: "We have no plans to make this a legislative requirement at this time."