Organisers of a protest outside Somerville House on Friday morning say students who attended have been given detention, a claim denied by the Presbyterian and Methodist Schools Association.
Close to 100 protesters gathered outside the school in a show of frustration with the PMSA, which is also responsible for Clayfield College, Brisbane Boys College and Sunshine Coast Grammar School.
The attendees ranged from pre-school age to grandparents and included a host of former students, as well as some uniformed students.
A spokesman for Beyond PMSA - a group leading the criticism of the PMSA in the wake of information leaks, a high-ranking school staffer's transfer to the overarching body and the standing down of principal Flo Kearney - said at least two students were given detention.
"As a parent, as a school, you'd be horrified. I mean, first the PMSA has intimidated a principal, teachers, parents, and now, the students," she said.
A PMSA spokesman denied the accusation.
"I just checked with the principal and she tells me that no student will be given detention for attending the protest this morning," he said.
The protest group is calling for the PMSA to be disbanded and for an independent inquiry into how it has been run, as well as greater transparency.
Speaking on ABC Radio Brisbane on Friday morning, PMSA chair Greg Adsett said all the organisation's decisions were made in the interests of "providing a united school community and providing stability".
"I couldn't answer to what their (the protesters') understanding is," he said.
"All I can say is that we as a PMSA are wanting to act in the best interests of our students and of our schools."
The protest came as the body hit back at growing concerns, denying any plans to centralise the management or administration of its four schools and playing down concerns relating to former Somerville House company secretary Rick Hiley meeting with former PMSA chair Robert McCall at a sauna, reportedly during school hours.
The association declared Mr Hiley had been cleared of any wrongdoing after downloading school information to a portable hard drive before leaving, saying it was needed for him to work from home.
"Mr Rick Hiley didn't do anything inappropriately," Mr Adsett said on radio.
A legal letter sent to the school's Parents and Friends' Association warned them not to discuss the 2015 Deloitte report, or they would face "appropriate" consequences.
On Thursday morning, former PFA president and former Somerville House board member Wendy Cox compared the statement to the work of famous fairytale writer Hans Christian Andersen.
"They're denying everything even though we know there are facts in place that say some of these things are absolutely correct," she said.
"If you think you can hide, you can't hide. We know where you are. Come on out and talk to us."