The school will begin talks with unions as it prepares to lose 3.6 full-time equivalent teaching jobs.
Commissioner Nicola Hornsey said yesterday a declining population in the area and the school's ''tarnished public image'' had contributed to the roll drop.
Ms Hornsey called a meeting of school staff yesterday morning after the Ministry of Education forecast the roll would drop 12.5% next year, from 474 pupils to 415.
The school's provisional staffing entitlement would reduce from 36.4 to 32.8.
Ms Hornsey said the roll prediction was concerning, particularly because of staffing implications.
''That's probably the biggest worry, because it does make people feel very unsettled and uncertain,'' she said.
''It's not an easy process for anybody to go through.''
Ms Hornsey said the school lost some pupils last year and ''based on the number of enrolments we have for next year, it looks like we'll be down against what we thought we would'', she said.
''It's been a culmination of events. It's not just something that's happened recently.''
The ministry appointed Ms Hornsey commissioner in October last year under its intervention process, after the school board of trustees stepped aside.
That followed two independent reports and an Education Review Office review that criticised the way the school was being governed and managed.
The school had to rebuild ''community confidence'', Ms Hornsey said.
''We have fantastic students at Waitaki Boys' and they're great ambassadors, and we have fantastic staff, so it's just a matter of the community being reassured and seeing signs of progress,'' she said.
Ms Hornsey said her primary focus had been on pupil wellbeing, both in the hostel and in the school. Significant changes and improvements had been made and the next step was raising pupil achievement.
School rector Paul Jackson said consultation with the unions - the Post Primary Teachers' Association and the New Zealand Educational Institute - would now start.
''We'll sit down and work out where we have extra staffing, what areas, and work from there,'' he said.
''It's always regrettable, but we have to move that way.''
The hostel had taken a big hit from the roll decline, Mr Jackson said.
''Usually, we bring in 24 students at a year 9 level and this year, we are nowhere near that mark at the moment, but there's time yet,'' he said.
At present, the hostel has 87 pupils, including 16 year 9 pupils.
''The boarding house, Don House, is the life and soul of the school, and we've got to keep our numbers up,'' Mr Jackson said.
''All boarding schools are chasing for students [as] the number of people who send their [children] to boarding school is dropping every year, so we've got to really keep up there.''
Plans to build a new boarding house at the school would still go ahead ''in the next few years''.
Mr Jackson said the community would probably feel the pinch of the projected roll drop, with reduced funding ($100,000), hostel income (about $300,000) and the losses of salaries of 3.6 teachers (about $262,000).
''That's quite a bit of money out of the community ... you're talking a cost to the community of more than half a million dollars,'' Mr Jackson said.
At co-ed St Kevin's College, in Oamaru, the roll is projected to remain at about 420 pupils next year.
''We are pleased to report a very positive outlook for the college, in that the current trend of enrolments puts us on par with the previous year,'' St Kevin's College principal Paul Olsen said.
