Ms Hornsey, named commissioner after the school's board of trustees stood down in October, has identified employment as a major issue.
''The school remains at risk in this area and significant time continues to be expended on addressing employment-related matters.''
It was one issue which led to the board of trustees stepping aside. Others ranged from management and governance to student discipline.
Yesterday, Ms Hornsey said two people from the New Zealand School Trustees' Association human resources division team had spent a day at the school reviewing employment issues, and were due back for another day.
The Otago Daily Times also understood an independent person had been brought in for staff appraisals, but Ms Hornsey said that came under management (rector Paul Jackson) and she could not comment.
The school had vacancies for an assistant principal - which was being readvertised - and two mainly part-time staff.
Since she had been appointed commissioner, three staff had resigned but exit interviews with Ms Hornsey found this was not because of school-related issues.
Asked if the school faced any Employment Relations Authority proceedings from staff, she said it did not.
However, she was unable to discuss whether the school was in mediation with any staff.
Last year, the Post Primary Teachers Association, the union which represented more than 20 teachers at the school, was at Waitaki Boys' to discuss what it viewed as a breach of the collective contract over non-contact time (time teachers have away from students for planning and other tasks).
Ms Hornsey said a revised timetable policy, which set out contract entitlements for non-contact time, was on the agenda for the next governance meeting after consultation with staff.
Another issue covered in a progress report was the effects of the statutory intervention on the school's financial position. The budget for 2015 showed a deficit.
''It is important that the costs of the intervention do not have a negative impact on the resourcing of teaching and learning, and so a detailed costs centre analysis will be undertaken prior to a provider being selected and engaged to conduct the forensic review,'' she said.
