The meeting was to discuss independent consultant Cleave Hay's issues report, commissioned after comments and criticism to the Ministry of Education about the way the school was being run.
Incidents date back to 2012, but were brought to a head last month when a senior staff member was stood down after an allegedly serious incident involving a pupil.
Board chairman Garry McLeod said yesterday the special meeting on Monday night was to discuss with Mr Hay the report's findings.
The public was excluded to protect the privacy of individuals.
The report was formally received by the board's regular meeting last night, again in public-excluded session for the same reason.
What Mr Hay's report contains will not be known until the board has fully considered it, and decided what, if anything, is eventually made public.
The Ministry of Education has a copy, but its head of sector enablement and support Katrina Casey, said it was up to the board to consider what to do.
''We ... will meet with the board after it has had time to consider the report, to discuss next steps. We will continue to provide support to the board as needed,'' she said.
This is not something that has suddenly hit the boys' school, which has a proud record going back to its foundation in 1883, producing some outstanding students and with a heritage reflected in its historic buildings.
Generations of boys from the same family have been among its pupils and there is a fierce loyalty to the school.
That loyalty remains among some parents and those associated with the school who say there are no major problems but a few stirring up trouble.
Others say people, particularly those related to pupils at the school, are afraid to speak out.
Then there are those who maintain the school is in crisis, and strong action is needed - possibly intervention by the Ministry to the extent of putting in a commissioner to manage it.
The present issues seem to have started two years ago, with comments and criticisms increasing until last month, when the Ministry of Education received 17 comments or criticisms, attended a closed board meeting and handed them over for the board to deal with, while it stayed in the wings observing.
The complaints relate to a wide range of issues including bullying and the treatment of pupils and teachers.
Other issues were pupil management, school communications, how the school managed concerns, policies being removed and not replaced and the wellbeing of pupils and staff.
Even the teachers' union, the Post Primary teachers' Association, got involved after an alleged breach of employment contract involving timetabling.
Specific issues, some said, were indicative of an over-arching problem with administration and management at the school.
Since about mid-2012 the school has lost a raft of teachers, including some senior staff with exceptional and long records at the school.
One was Graham Kitchin (61), who retired early from the school after 38 years, at the end of 2012, because of management issues he felt were not likely to improve.
Another was Priscilla Hay, who taught at the school for 10 years, including four years as head of science.
She first raised her concerns over management and administration at the school in mid-2012, and again when she left after obtaining a lesser role as a long-term relieving teacher in Tauranga in November.
Complaints have also come from other teachers, pupils' parents and people within the wider school community.
